Variant report

Variant	rs3130283
Chromosome Location	chr6:32138545-32138546
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:32116953..32128256-chr6:32128373..32148325,54	K562	blood:
2	chr6:32137753..32139560-chr6:32162368..32164266,2	MCF-7	breast:
3	chr6:32054009..32055656-chr6:32135813..32138585,2	K562	blood:
4	chr6:32119715..32123835-chr6:32132075..32139187,7	MCF-7	breast:
5	chr6:32133333..32138602-chr6:32161544..32165617,8	K562	blood:
6	chr6:31939663..31941212-chr6:32136845..32139340,2	K562	blood:

Variant related genes	Relation type
ENSG00000213654	Chromatin interaction
ENSG00000204344	Chromatin interaction
ENSG00000204301	Chromatin interaction
ENSG00000204348	Chromatin interaction
ENSG00000258388	Chromatin interaction
ENSG00000204314	Chromatin interaction
ENSG00000221988	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1044506	0.84[EUR][1000 genomes]
rs1800684	0.95[EUR][1000 genomes]
rs204996	0.85[ASN][1000 genomes]
rs2853807	0.85[ASN][1000 genomes]
rs3117182	0.84[AMR][1000 genomes]
rs3117189	0.84[AMR][1000 genomes]
rs3130279	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130287	0.84[AMR][1000 genomes]
rs3130342	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131283	0.88[EUR][1000 genomes]
rs3131294	0.82[EUR][1000 genomes]
rs3132940	0.86[EUR][1000 genomes]
rs3134603	0.87[EUR][1000 genomes]
rs3134604	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134943	0.91[EUR][1000 genomes]
rs3134954	0.84[AMR][1000 genomes];0.81[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	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
37	nsv884707	chr6:32132233-32146492	Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3130283	HLA-DRB5	cis	parietal	SCAN
rs3130283	HLA-DRB1///LOC730415	N/A	lymphoblastoid	RTeQTL
rs3130283	LEMD2	cis	cerebellum	SCAN
rs3130283	HLA-DQB1	cis	lymphoblastoid	GTEx
rs3130283	HLA-DQA1	cis	lymphoblastoid	GTEx
rs3130283	HLA-DRB5	cis	lymphoblastoid	GTEx
rs3130283	HLA.DRB5	cis	multi-tissue	Pritchard
rs3130283	HLA-DQB1	cis	lymphoblastoid	seeQTL
rs3130283	HLA-C	cis	lymphoblastoid	GTEx
rs3130283	HLA-DRB5	cis	lymphoblastoid	seeQTL
rs3130283	HLA-DRB5	cis	cerebellum	SCAN
rs3130283	HLA-DRB6	cis	lymphoblastoid	seeQTL
rs3130283	HLA-DQA2	cis	lymphoblastoid	seeQTL
rs3130283	HLA-DRB1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:32123200-32142200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:32123200-32142200	Weak transcription	Small Intestine	intestine
3	chr6:32123200-32142600	Weak transcription	Psoas Muscle	Psoas
4	chr6:32123200-32142600	Weak transcription	HUVEC	blood vessel
5	chr6:32123600-32139400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:32123600-32139800	Strong transcription	Fetal Stomach	stomach
7	chr6:32123600-32140600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:32123800-32140600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:32123800-32140600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:32126000-32140400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:32126400-32138600	Weak transcription	Fetal Brain Male	brain
12	chr6:32126600-32140800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:32126600-32142600	Weak transcription	Fetal Kidney	kidney
14	chr6:32127000-32140600	Weak transcription	Hela-S3	cervix
15	chr6:32129600-32139200	Strong transcription	Ovary	ovary
16	chr6:32129600-32139400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:32129800-32139400	Strong transcription	Fetal Brain Female	brain
18	chr6:32130000-32139800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:32130000-32140000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:32130200-32139400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:32130200-32139400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:32130400-32139400	Strong transcription	Liver	Liver
23	chr6:32130400-32139400	Strong transcription	Brain Germinal Matrix	brain
24	chr6:32130400-32140200	Strong transcription	HepG2	liver
25	chr6:32132200-32139400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:32132200-32139400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr6:32132200-32139400	Strong transcription	Right Ventricle	heart
28	chr6:32132200-32140000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:32133000-32140800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:32133200-32139600	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr6:32133400-32139200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:32133400-32139400	Strong transcription	Adipose Nuclei	Adipose
33	chr6:32133400-32139400	Strong transcription	NHLF	lung
34	chr6:32133600-32139000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:32133600-32139200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:32133600-32139200	Strong transcription	Brain Substantia Nigra	brain
37	chr6:32133600-32139200	Strong transcription	Colon Smooth Muscle	Colon
38	chr6:32133600-32139200	Strong transcription	Lung	lung
39	chr6:32133600-32139200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr6:32133600-32139200	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:32133600-32139200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:32133600-32139200	Strong transcription	Thymus	Thymus
43	chr6:32133600-32139400	Strong transcription	Fetal Thymus	thymus
44	chr6:32133600-32139400	Strong transcription	Dnd41	blood
45	chr6:32133600-32139800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr6:32133600-32141200	Strong transcription	Fetal Lung	lung
47	chr6:32133800-32138800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:32133800-32139200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:32133800-32139200	Strong transcription	Esophagus	oesophagus
50	chr6:32133800-32139400	Strong transcription	Primary T cells from cord blood	blood

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