Variant report

Variant	rs3811087
Chromosome Location	chr6:142409969-142409970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr6:142409718-142410575	A549	lung:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
2	REST	chr6:142409953-142410457	A549	lung:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
3	TEAD4	chr6:142409864-142410537	A549	lung:	n/a	n/a
4	SIN3AK20	chr6:142409810-142410543	MCF-7	breast:	n/a	n/a
5	REST	chr6:142409924-142410463	PFSK-1	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
6	CTCF	chr6:142409880-142410030	HEK293	kidney:	n/a	n/a
7	MAX	chr6:142409961-142410409	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr6:142409784-142410443	SK-N-SH	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
9	MAX	chr6:142409936-142410304	ECC-1	luminal epithelium:	n/a	n/a
10	BACH1	chr6:142409948-142410277	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr6:142409635-142410611	MCF-7	breast:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
12	REST	chr6:142409654-142410759	HL-60	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
13	RCOR1	chr6:142409815-142410450	IMR90	lung:	n/a	n/a
14	HDAC2	chr6:142409918-142410421	MCF-7	breast:	n/a	n/a
15	REST	chr6:142409698-142410745	MCF-7	breast:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
16	REST	chr6:142409857-142410504	PFSK-1	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
17	REST	chr6:142409898-142410530	HL-60	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
18	REST	chr6:142409922-142410454	K562	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
19	SIN3AK20	chr6:142409949-142410406	MCF-7	breast:	n/a	n/a
20	GATA3	chr6:142409949-142410276	T-47D	breast:	n/a	n/a
21	YY1	chr6:142409967-142410341	H1-hESC	embryonic stem cell:	n/a	chr6:142410244-142410258
22	SPI1	chr6:142409922-142410414	HL-60	blood:	n/a	n/a
23	REST	chr6:142409722-142410484	H1-hESC	embryonic stem cell:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
24	MAX	chr6:142409938-142410436	MCF-7	breast:	n/a	n/a
25	REST	chr6:142409808-142410510	HepG2	liver:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
26	ATF2	chr6:142409951-142410378	H1-hESC	embryonic stem cell:	n/a	n/a
27	REST	chr6:142409666-142410760	ECC-1	luminal epithelium:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
28	REST	chr6:142409600-142410509	H1-hESC	embryonic stem cell:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
29	REST	chr6:142409760-142410444	PANC-1	pancreas:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
30	REST	chr6:142409657-142410749	ECC-1	luminal epithelium:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
31	REST	chr6:142409847-142410411	HepG2	liver:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
32	REST	chr6:142409572-142410552	SK-N-SH	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
33	SIN3A	chr6:142409920-142410404	H1-hESC	embryonic stem cell:	n/a	chr6:142410201-142410210 chr6:142410134-142410142 chr6:142410204-142410217 chr6:142410135-142410148
34	REST	chr6:142409897-142410457	GM12878	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
35	REST	chr6:142409682-142410606	PANC-1	pancreas:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
36	REST	chr6:142409761-142410608	PANC-1	pancreas:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
37	SIN3AK20	chr6:142409963-142410321	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:142409939-142409989	HEK293	kidney:	embryo
2	chr6:142409939-142409989	Hela-S3	cervix:	n/a
3	chr6:142409939-142409989	HMEC	breast:	n/a
4	chr6:142409939-142409989	GM12891	blood:	n/a
5	chr6:142409939-142409989	BJ	skin:	n/a
6	chr6:142409939-142409989	GM06990	blood:	n/a
7	chr6:142409939-142409989	CMK	blood:	n/a
8	chr6:142409939-142409989	HCPEpiC	choroid plexus:	n/a
9	chr6:142409939-142409989	SK-N-MC	brain:	n/a
10	chr6:142409939-142409989	HRE	kidney:	n/a
11	chr6:142409939-142409989	LNCaP	prostate:	n/a
12	chr6:142409939-142409989	MCF-7	breast:	n/a
13	chr6:142409939-142409989	IMR90	lung:	fetal
14	chr6:142409939-142409989	HEEpiC	esophagus:	n/a
15	chr6:142409939-142409989	PANC-1	pancreas:	n/a
16	chr6:142409939-142409989	Hepatocyte	liver:	n/a
17	chr6:142409939-142409989	ProgFib	skin:	n/a
18	chr6:142409939-142409989	HNPCEpiC	eye:	n/a
19	chr6:142409939-142409989	NB4	blood:	n/a
20	chr6:142409939-142409989	HUVEC	blood vessel:	n/a
21	chr6:142409939-142409989	T-47D	breast:	n/a
22	chr6:142409939-142409989	Jurkat	blood:	n/a
23	chr6:142409939-142409989	AG04449	skin:	fetal
24	chr6:142409939-142409989	HIPEpiC	eye:	n/a
25	chr6:142409939-142409989	K562	blood:	n/a
26	chr6:142409939-142409989	NHDF-neo	bronchial:	n/a
27	chr6:142409939-142409989	HCT-116	colon:	n/a
28	chr6:142409939-142409989	GM19239	blood:	n/a
29	chr6:142409939-142409989	HRCEpiC	kidney:	n/a
30	chr6:142409939-142409989	NHBE	bronchial:	n/a
31	chr6:142409939-142409989	A549	lung:	n/a
32	chr6:142409939-142409989	AG09309	skin:	n/a
33	chr6:142409939-142409989	ovcar-3	ovarian:	n/a
34	chr6:142409939-142409989	AG10803	skin:	n/a
35	chr6:142409939-142409989	ECC-1	luminal epithelium:	n/a
36	chr6:142409939-142409989	GM12878	blood:	n/a
37	chr6:142409939-142409989	HepG2	liver:	n/a
38	chr6:142409939-142409989	U87	brain:	n/a
39	chr6:142409939-142409989	HCM	heart:	n/a
40	chr6:142409939-142409989	AG09319	gingival:	n/a
41	chr6:142409939-142409989	H1-hESC	embryonic stem cell:	embryo
42	chr6:142409939-142409989	HRPEpiC	eye:	n/a
43	chr6:142409939-142409989	RPTEC	kidney:	n/a
44	chr6:142409939-142409989	AG04450	lung:	fetal
45	chr6:142409939-142409989	MCF10A-Er-Src	breast:	n/a
46	chr6:142409939-142409989	HL-60	blood:	n/a
47	chr6:142409939-142409989	GM12892	blood:	n/a
48	chr6:142409939-142409989	SKMC	muscle:	n/a
49	chr6:142409939-142409989	BE2_C	brain:	n/a
50	chr6:142409939-142409989	NT2-D1	testis:	n/a

Variant related genes	Relation type
NMBR	TF binding region
NMBR	CpG island

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10485027	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12661511	0.92[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12665758	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap]
rs17071411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17071541	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1835	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6931975	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7453944	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761155	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9496261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1027489	chr6:142336722-142429903	Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv886735	chr6:142365171-142472294	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3811087	VTA1	cis	lymphoblastoid	seeQTL
rs3811087	VTA1	cis	multi-tissue	Pritchard
rs3811087	VTA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142409200-142410000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:142409200-142410200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
3	chr6:142409200-142410200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr6:142409200-142410200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:142409200-142410200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:142409200-142410200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:142409200-142410200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:142409200-142410200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:142409200-142410200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:142409200-142410400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:142409400-142410000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
12	chr6:142409400-142410000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr6:142409400-142410000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:142409400-142410000	Bivalent Enhancer	Esophagus	oesophagus
15	chr6:142409400-142410200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr6:142409400-142410200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
17	chr6:142409400-142410400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:142409400-142410400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
19	chr6:142409600-142410000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:142409600-142410000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:142409600-142410000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:142409600-142410000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:142409600-142410000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
24	chr6:142409600-142410000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:142409600-142410000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:142409600-142410000	Bivalent Enhancer	Liver	Liver
27	chr6:142409600-142410000	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr6:142409600-142410000	Bivalent Enhancer	Left Ventricle	heart
29	chr6:142409600-142410000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
30	chr6:142409600-142410000	Enhancers	Right Atrium	heart
31	chr6:142409600-142410000	Bivalent Enhancer	HSMMtube	muscle
32	chr6:142409600-142410200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:142409600-142410200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
34	chr6:142409600-142410200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
35	chr6:142409600-142410200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
36	chr6:142409600-142410400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:142409600-142410400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
38	chr6:142409600-142410400	Bivalent Enhancer	Ovary	ovary
39	chr6:142409800-142410000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:142409800-142410000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:142409800-142410000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:142409800-142410000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:142409800-142410000	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
44	chr6:142409800-142410000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
45	chr6:142409800-142410000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
46	chr6:142409800-142410000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:142409800-142410000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:142409800-142410000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:142409800-142410000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
50	chr6:142409800-142410000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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