Variant report

Variant	rs3134603
Chromosome Location	chr6:32126002-32126003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:32125935-32126125	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:32121547..32123431-chr6:32124624..32127315,2	MCF-7	breast:
2	chr6:32120171..32123942-chr6:32124306..32127652,6	K562	blood:
3	chr6:32095682..32098232-chr6:32125568..32127068,2	MCF-7	breast:
4	chr6:32116953..32128256-chr6:32128373..32148325,54	K562	blood:
5	chr6:32123472..32127335-chr6:32140549..32144083,4	MCF-7	breast:
6	chr6:32117819..32120685-chr6:32124455..32126821,3	MCF-7	breast:
7	chr6:32118687..32120696-chr6:32125544..32127765,2	MCF-7	breast:
8	chr6:32120233..32126271-chr6:32158822..32166984,18	K562	blood:
9	chr6:32093775..32101330-chr6:32116233..32126080,28	K562	blood:
10	chr6:32124310..32127187-chr6:32144126..32145927,3	MCF-7	breast:
11	chr6:32121385..32123700-chr6:32124923..32127275,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRRT1	TF binding region
ENSG00000221988	Chromatin interaction
ENSG00000213654	Chromatin interaction
ENSG00000213676	Chromatin interaction
ENSG00000204308	Chromatin interaction
ENSG00000204315	Chromatin interaction
ENSG00000258388	Chromatin interaction
ENSG00000241404	Chromatin interaction
ENSG00000204301	Chromatin interaction
ENSG00000204314	Chromatin interaction
ENSG00000204310	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1800684	0.82[EUR][1000 genomes]
rs3130279	0.84[EUR][1000 genomes]
rs3130283	0.87[EUR][1000 genomes]
rs3130346	0.96[EUR][1000 genomes]
rs3134604	0.96[EUR][1000 genomes]
rs3134943	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:37 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv601950	chr6:31785438-32492308	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
3	nsv601951	chr6:31785438-32496748	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
4	nsv601955	chr6:31785453-32484368	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
5	nsv601956	chr6:31785453-32492308	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
6	nsv601961	chr6:31868322-32484368	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	esv2758043	chr6:31871512-32209113	Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
8	esv2759415	chr6:31871512-32209113	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
9	nsv601972	chr6:31947594-32484368	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv601975	chr6:31949352-32484368	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
11	nsv601976	chr6:31949352-32508887	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
12	nsv601977	chr6:31949352-32651056	Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
13	nsv601980	chr6:31950266-32484368	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv601982	chr6:31951207-32484368	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
15	nsv601983	chr6:31951367-32484368	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
16	nsv601984	chr6:31951912-32484368	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
17	nsv601999	chr6:31952422-32484368	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
18	nsv602000	chr6:31952422-32552416	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
19	nsv602015	chr6:31953467-32481507	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
20	nsv602016	chr6:31953467-32484368	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
21	nsv602017	chr6:31953467-32505730	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
22	nsv602018	chr6:31953467-32509985	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
23	nsv602019	chr6:31953467-32779803	Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
24	nsv602029	chr6:31955572-32484368	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
25	nsv602035	chr6:31959480-32484368	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
26	nsv602036	chr6:31959878-32484368	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
27	nsv602052	chr6:31972034-32481507	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
28	nsv602053	chr6:31972034-32484368	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
29	nsv602054	chr6:31972034-32779803	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
30	nsv602086	chr6:31986320-32484368	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
31	nsv1024599	chr6:32007556-32481240	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
32	nsv830629	chr6:32043978-32189787	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
33	nsv1033939	chr6:32048657-32196256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
34	nsv462876	chr6:32064726-32171683	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
35	nsv602104	chr6:32064726-32171683	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
36	nsv884701	chr6:32089549-32130329	Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
37	nsv884706	chr6:32116313-32146492	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3134603	HLA-DRB5	cis	lymphoblastoid	GTEx
rs3134603	HLA-DQB1	cis	lymphoblastoid	GTEx
rs3134603	HLA-DRB5	cis	cerebellum	SCAN
rs3134603	HLA-DRB5	cis	lymphoblastoid	seeQTL
rs3134603	LEMD2	cis	cerebellum	SCAN
rs3134603	HLA-C	cis	lymphoblastoid	GTEx
rs3134603	HLA-DRB5	cis	parietal	SCAN
rs3134603	HLA-DRB1	cis	lymphoblastoid	seeQTL
rs3134603	HLA.DRB5	cis	multi-tissue	Pritchard
rs3134603	HLA-DRB1///LOC730415	N/A	lymphoblastoid	RTeQTL
rs3134603	HLA-DQB1	cis	lymphoblastoid	seeQTL
rs3134603	HLA-DQA1	cis	lymphoblastoid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:32122600-32134400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:32123000-32131600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:32123000-32134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:32123200-32126200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:32123200-32126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr6:32123200-32135000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:32123200-32136200	Weak transcription	GM12878-XiMat	blood
8	chr6:32123200-32136400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:32123200-32142200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:32123200-32142200	Weak transcription	Small Intestine	intestine
11	chr6:32123200-32142600	Weak transcription	Psoas Muscle	Psoas
12	chr6:32123200-32142600	Weak transcription	HUVEC	blood vessel
13	chr6:32123400-32126800	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr6:32123400-32127000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:32123400-32127200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:32123400-32127600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:32123400-32135000	Weak transcription	Right Atrium	heart
18	chr6:32123400-32135600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:32123600-32126800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr6:32123600-32126800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:32123600-32126800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:32123600-32126800	Strong transcription	Brain Angular Gyrus	brain
23	chr6:32123600-32126800	Strong transcription	Brain Anterior Caudate	brain
24	chr6:32123600-32126800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:32123600-32126800	Strong transcription	Placenta	Placenta
26	chr6:32123600-32126800	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr6:32123600-32126800	Strong transcription	Thymus	Thymus
28	chr6:32123600-32127000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:32123600-32127000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:32123600-32127000	Strong transcription	Brain Cingulate Gyrus	brain
31	chr6:32123600-32127000	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr6:32123600-32127000	Strong transcription	Left Ventricle	heart
33	chr6:32123600-32127400	Strong transcription	Fetal Thymus	thymus
34	chr6:32123600-32127600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:32123600-32130600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr6:32123600-32130800	Weak transcription	Colonic Mucosa	Colon
37	chr6:32123600-32131600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:32123600-32134000	Weak transcription	Pancreas	Pancrea
39	chr6:32123600-32135000	Weak transcription	Fetal Heart	heart
40	chr6:32123600-32136000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr6:32123600-32136600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:32123600-32137200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:32123600-32139400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:32123600-32139800	Strong transcription	Fetal Stomach	stomach
45	chr6:32123600-32140600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:32123800-32126200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr6:32123800-32126400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr6:32123800-32126600	Strong transcription	Fetal Kidney	kidney
49	chr6:32123800-32126800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:32123800-32126800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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