Variant report

Variant	rs2269425
Chromosome Location	chr6:32123639-32123640
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:14)
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	chr6:32123219-32123748	HepG2	liver:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:32120171..32123942-chr6:32124306..32127652,6	K562	blood:
2	chr6:32119715..32123835-chr6:32132075..32139187,7	MCF-7	breast:
3	chr6:32093127..32099788-chr6:32117635..32125818,23	K562	blood:
4	chr6:31867782..31870627-chr6:32121344..32123906,2	K562	blood:
5	chr6:32121385..32123700-chr6:32124923..32127275,2	MCF-7	breast:
6	chr6:32093545..32101236-chr6:32120105..32124952,17	MCF-7	breast:
7	chr6:32086044..32088268-chr6:32122261..32123962,3	MCF-7	breast:
8	chr6:32116953..32128256-chr6:32128373..32148325,54	K562	blood:
9	chr6:32123472..32127335-chr6:32140549..32144083,4	MCF-7	breast:
10	chr6:32081881..32084783-chr6:32122439..32124019,2	K562	blood:
11	chr6:32122184..32124281-chr6:32133755..32136302,3	MCF-7	breast:
12	chr6:32120233..32126271-chr6:32158822..32166984,18	K562	blood:
13	chr6:32093775..32101330-chr6:32116233..32126080,28	K562	blood:
14	chr6:32085766..32089090-chr6:32120902..32124817,4	K562	blood:

No data

Variant related genes	Relation type
PPT2	TF binding region
PPT2-EGFL8	TF binding region
PRRT1	TF binding region
ENSG00000204310	Chromatin interaction
ENSG00000213654	Chromatin interaction
ENSG00000204308	Chromatin interaction
ENSG00000168477	Chromatin interaction
ENSG00000213676	Chromatin interaction
ENSG00000204315	Chromatin interaction
ENSG00000204366	Chromatin interaction
ENSG00000221988	Chromatin interaction
ENSG00000204301	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000241404	Chromatin interaction
ENSG00000258388	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12524510	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16869385	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9296009	0.84[ASN][1000 genomes]
rs9469089	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2269425	SRPK1	cis	parietal	SCAN
rs2269425	PRDM16	trans	parietal	SCAN
rs2269425	LEMD2	cis	parietal	SCAN

Chromatin state (count:121 , 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	chr6:32122800-32123800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:32122800-32123800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:32122800-32123800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:32123000-32123800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr6:32123000-32123800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:32123000-32123800	Enhancers	Lung	lung
8	chr6:32123000-32125400	Weak transcription	Aorta	Aorta
9	chr6:32123000-32126000	Weak transcription	A549	lung
10	chr6:32123000-32131600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:32123000-32134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:32123200-32123800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:32123200-32123800	Genic enhancers	Primary T cells from cord blood	blood
14	chr6:32123200-32123800	Enhancers	Primary hematopoietic stem cells	blood
15	chr6:32123200-32123800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr6:32123200-32123800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr6:32123200-32123800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:32123200-32123800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:32123200-32123800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:32123200-32123800	Genic enhancers	Liver	Liver
21	chr6:32123200-32123800	Genic enhancers	Brain Hippocampus Middle	brain
22	chr6:32123200-32123800	Genic enhancers	Fetal Brain Female	brain
23	chr6:32123200-32123800	Genic enhancers	Fetal Intestine Large	intestine
24	chr6:32123200-32123800	Genic enhancers	Fetal Muscle Leg	muscle
25	chr6:32123200-32123800	Enhancers	Stomach Mucosa	stomach
26	chr6:32123200-32123800	Genic enhancers	HepG2	liver
27	chr6:32123200-32123800	Enhancers	HMEC	breast
28	chr6:32123200-32124200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:32123200-32124400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr6:32123200-32124600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:32123200-32125400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:32123200-32125400	Weak transcription	HSMM	muscle
33	chr6:32123200-32125400	Weak transcription	HSMMtube	muscle
34	chr6:32123200-32126200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:32123200-32126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:32123200-32135000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr6:32123200-32136200	Weak transcription	GM12878-XiMat	blood
38	chr6:32123200-32136400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:32123200-32142200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:32123200-32142200	Weak transcription	Small Intestine	intestine
41	chr6:32123200-32142600	Weak transcription	Psoas Muscle	Psoas
42	chr6:32123200-32142600	Weak transcription	HUVEC	blood vessel
43	chr6:32123400-32123800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:32123400-32123800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:32123400-32123800	Genic enhancers	Esophagus	oesophagus
46	chr6:32123400-32123800	Genic enhancers	Fetal Intestine Small	intestine
47	chr6:32123400-32123800	Genic enhancers	Fetal Kidney	kidney
48	chr6:32123400-32123800	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr6:32123400-32123800	Genic enhancers	Rectal Mucosa Donor 31	rectum
50	chr6:32123400-32123800	Genic enhancers	Skeletal Muscle Male	skeletal muscle

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