Variant report

Variant	rs9461625
Chromosome Location	chr6:30695239-30695240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30687036-30695449	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr6:30683610-30695318	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr6:30690112-30695297	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:30687488-30695337	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr6:30692338-30695323	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr6:30692209-30696227	U87	brain:	n/a	n/a
7	POLR2A	chr6:30687419-30696083	PFSK-1	brain:	n/a	n/a
8	PML	chr6:30692136-30695252	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:30690124-30695305	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr6:30690069-30695502	MCF-7	breast:	n/a	n/a
11	POLR2A	chr6:30690223-30696218	A549	lung:	n/a	n/a
12	MTA3	chr6:30692389-30695265	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:30692414-30696242	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr6:30686133-30696545	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr6:30686246-30695327	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:30687079-30696265	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr6:30694862-30695425	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:30692187-30695320	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr6:30690138-30695256	K562	blood:	n/a	n/a
20	POLR2A	chr6:30687427-30695328	GM12892	blood:	n/a	n/a
21	POLR2A	chr6:30692203-30695325	U87	brain:	n/a	n/a
22	POLR2A	chr6:30687078-30695465	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr6:30692164-30695290	HUVEC	blood vessel:	n/a	n/a
24	JUND	chr6:30692621-30695288	SK-N-SH	brain:	n/a	chr6:30694919-30694928 chr6:30693232-30693243
25	POLR2A	chr6:30690201-30696224	K562	blood:	n/a	n/a
26	POLR2A	chr6:30687000-30696307	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr6:30687173-30696145	HepG2	liver:	n/a	n/a
28	POLR2A	chr6:30694933-30696307	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30694053..30695767-chr6:31049504..31051696,2	K562	blood:
2	chr6:30694636..30696358-chr6:30788592..30791356,2	K562	blood:
3	chr6:30694210..30695985-chr6:30745346..30747310,2	K562	blood:
4	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
5	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
6	chr6:30693361..30695767-chr6:30895208..30897558,2	K562	blood:
7	chr6:30592689..30594300-chr6:30694782..30696662,2	MCF-7	breast:
8	chr6:30693275..30696224-chr6:30778287..30780136,2	K562	blood:
9	chr6:30692887..30695267-chr6:30900165..30903279,3	K562	blood:
10	chr6:30623054..30625319-chr6:30693662..30695585,2	K562	blood:
11	chr6:30693700..30695786-chr6:32145434..32148332,2	MCF-7	breast:
12	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
13	chr6:30693489..30695264-chr6:30866666..30869392,2	K562	blood:
14	chr6:30614239..30616537-chr6:30694682..30697216,2	MCF-7	breast:
15	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
16	chr6:30638735..30640810-chr6:30694187..30696217,2	MCF-7	breast:
17	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272540	TF binding region
ENSG00000222894	Chromatin interaction
ENSG00000230449	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204308	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000252761	Chromatin interaction
ENSG00000222895	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000204310	Chromatin interaction
ENSG00000137404	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1109146	0.82[EUR][1000 genomes]
rs16867852	0.82[EUR][1000 genomes]
rs16897781	0.82[EUR][1000 genomes]
rs16897791	0.82[EUR][1000 genomes]
rs2075015	0.82[EUR][1000 genomes]
rs2269702	0.82[EUR][1000 genomes]
rs2269707	0.82[EUR][1000 genomes]
rs2284172	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285321	0.82[EUR][1000 genomes]
rs25497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28986465	0.82[EUR][1000 genomes]
rs55810373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57928524	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61486053	0.82[EUR][1000 genomes]
rs6929698	0.82[EUR][1000 genomes]
rs6931293	0.82[EUR][1000 genomes]
rs6937357	0.82[EUR][1000 genomes]
rs73727463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295902	0.82[EUR][1000 genomes]
rs9295904	0.82[EUR][1000 genomes]
rs9295905	0.82[EUR][1000 genomes]
rs9295908	0.82[EUR][1000 genomes]
rs9461620	0.82[EUR][1000 genomes]
rs9461622	0.82[EUR][1000 genomes]
rs9461623	0.82[EUR][1000 genomes]
rs9461624	0.82[EUR][1000 genomes]
rs9468803	0.82[EUR][1000 genomes]
rs9468805	0.82[EUR][1000 genomes]
rs9468811	0.82[EUR][1000 genomes]
rs9468813	0.82[EUR][1000 genomes]
rs9468816	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468821	0.85[AFR][1000 genomes]
rs9468822	0.85[AFR][1000 genomes]
rs9500863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9500864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9500865	0.85[AFR][1000 genomes]
rs9500866	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9500867	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9501027	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9501338	0.82[EUR][1000 genomes]
rs9501484	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription 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	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS 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	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv970736	chr6:30692055-30710740	Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30690000-30709600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30690200-30699200	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:30690400-30696400	Strong transcription	Gastric	stomach
4	chr6:30690400-30709200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:30690600-30698000	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr6:30690600-30698200	Strong transcription	Left Ventricle	heart
7	chr6:30690600-30698400	Strong transcription	Right Ventricle	heart
8	chr6:30690600-30701200	Strong transcription	Brain Angular Gyrus	brain
9	chr6:30690600-30703800	Strong transcription	Lung	lung
10	chr6:30691000-30697800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:30691000-30698000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:30691000-30698000	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:30691000-30698200	Strong transcription	Fetal Intestine Large	intestine
14	chr6:30691000-30698400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:30691000-30698400	Strong transcription	Brain Anterior Caudate	brain
16	chr6:30691000-30698400	Strong transcription	Brain Hippocampus Middle	brain
17	chr6:30691000-30703800	Strong transcription	Brain Cingulate Gyrus	brain
18	chr6:30691200-30697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:30691200-30697800	Strong transcription	Placenta	Placenta
20	chr6:30691600-30696200	Strong transcription	Thymus	Thymus
21	chr6:30691600-30698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:30691600-30698000	Strong transcription	Fetal Intestine Small	intestine
23	chr6:30691800-30698000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr6:30692000-30695600	Weak transcription	Ovary	ovary
25	chr6:30692000-30697400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:30692000-30698200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:30692000-30698200	Strong transcription	Colonic Mucosa	Colon
28	chr6:30692200-30697200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:30692200-30698200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr6:30692400-30695600	Weak transcription	Stomach Mucosa	stomach
31	chr6:30692400-30695800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:30692400-30697600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:30692600-30695600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:30692600-30708200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:30693000-30695600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:30693000-30695600	Strong transcription	Liver	Liver
37	chr6:30693000-30696200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:30693000-30698000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:30693000-30698000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr6:30693200-30695600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:30693200-30695800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr6:30693200-30696200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:30693200-30697200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:30693200-30697400	Weak transcription	Psoas Muscle	Psoas
45	chr6:30693200-30698200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:30693200-30698200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr6:30693200-30698400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:30693200-30708800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:30693400-30695400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr6:30693400-30698400	Strong transcription	Rectal Mucosa Donor 29	rectum

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