Variant report

Variant	rs7622851
Chromosome Location	chr3:52333671-52333672
allele	C/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	POLR2A	chr3:52327536-52335341	HepG2	liver:	n/a	n/a
2	JUND	chr3:52333589-52333729	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:52332459-52334382	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr3:52326828-52335551	HepG2	liver:	n/a	n/a
5	ZNF263	chr3:52333501-52334482	HEK293-T-REx	kidney:	n/a	chr3:52333899-52333920 chr3:52333876-52333897
6	POLR2A	chr3:52333663-52333727	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:52330489-52334598	HepG2	liver:	n/a	n/a
8	CTBP2	chr3:52333234-52334460	H1-hESC	embryonic stem cell:	n/a	n/a
9	ELF1	chr3:52333398-52334355	GM12878	blood:	n/a	n/a
10	CHD2	chr3:52333292-52333696	HepG2	liver:	n/a	n/a
11	STAT5A	chr3:52333477-52334313	GM12878	blood:	n/a	n/a
12	MTA3	chr3:52333136-52334687	GM12878	blood:	n/a	n/a
13	NFATC1	chr3:52333581-52334473	GM12878	blood:	n/a	n/a
14	ELF1	chr3:52333473-52333694	K562	blood:	n/a	n/a
15	POLR2A	chr3:52333618-52334365	H1-neurons	neurons:	n/a	n/a
16	RUNX3	chr3:52333626-52334425	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:52326795-52334549	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:52333611-52334582	GM12878	blood:	n/a	n/a
19	ZBTB7A	chr3:52333520-52333701	K562	blood:	n/a	n/a
20	ZNF143	chr3:52333308-52334334	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:52333578-52334534	HL-60	blood:	n/a	n/a
22	POLR2A	chr3:52333580-52334685	K562	blood:	n/a	n/a
23	RCOR1	chr3:52333492-52333724	K562	blood:	n/a	n/a
24	POLR2A	chr3:52333648-52333839	GM12878	blood:	n/a	n/a
25	TAF1	chr3:52332634-52334299	H1-neurons	neurons:	n/a	n/a
26	REST	chr3:52331995-52334516	H1-neurons	neurons:	n/a	chr3:52334239-52334252 chr3:52334242-52334255 chr3:52334249-52334259 chr3:52332509-52332529 chr3:52334190-52334203 chr3:52332675-52332685 chr3:52334119-52334132
27	POLR2A	chr3:52333669-52334667	K562	blood:	n/a	n/a
28	POLR2A	chr3:52333329-52334539	HepG2	liver:	n/a	n/a
29	POLR2A	chr3:52333652-52334637	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52328227..52330124-chr3:52332267..52334731,2	MCF-7	breast:
2	chr3:52321744..52323842-chr3:52332822..52334732,2	MCF-7	breast:

Variant related genes	Relation type
GLYCTK-AS1	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000207926	Chromatin interaction
ENSG00000168237	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1060330	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1077142	0.95[YRI][hapmap]
rs11705963	0.84[AFR][1000 genomes]
rs11706108	0.84[AFR][1000 genomes]
rs11717383	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13091545	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs13094687	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs164640	0.87[JPT][hapmap]
rs181274	0.87[JPT][hapmap]
rs187084	0.87[JPT][hapmap]
rs2272088	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2276834	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34228726	0.86[ASN][1000 genomes]
rs34569561	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs352139	0.87[JPT][hapmap]
rs352140	0.87[JPT][hapmap]
rs352162	0.87[JPT][hapmap]
rs352163	0.87[JPT][hapmap]
rs352165	0.87[JPT][hapmap]
rs352166	0.87[JPT][hapmap]
rs352167	0.87[JPT][hapmap]
rs352168	0.87[JPT][hapmap]
rs352169	0.87[JPT][hapmap]
rs352170	0.87[JPT][hapmap]
rs353547	0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs35860312	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs3844291	0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs3852063	0.89[ASN][1000 genomes]
rs3852064	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs498946	0.87[YRI][hapmap]
rs57615517	0.85[ASN][1000 genomes]
rs57630131	0.81[ASN][1000 genomes]
rs59565798	0.85[ASN][1000 genomes]
rs610060	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6445358	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs648514	0.85[CEU][hapmap]
rs66462821	0.82[AFR][1000 genomes]
rs6794675	0.84[AFR][1000 genomes]
rs730050	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7614727	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618915	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7629072	0.80[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643570	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs9311474	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS 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 miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS 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	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7622851	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs7622851	FLJ12442	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
2	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
3	chr3:52325600-52340400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:52327200-52333800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
6	chr3:52327400-52338400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
8	chr3:52327600-52334000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:52327600-52344600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:52327800-52333800	Weak transcription	Esophagus	oesophagus
11	chr3:52328000-52334200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:52328000-52337000	Weak transcription	Adipose Nuclei	Adipose
13	chr3:52328000-52347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:52328200-52334200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:52328200-52340200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
17	chr3:52328600-52340000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:52328800-52340200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
20	chr3:52329000-52334400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:52330000-52335000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:52330200-52334600	Enhancers	Primary hematopoietic stem cells	blood
24	chr3:52330200-52343400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:52330200-52343400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:52330200-52345400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:52331000-52337600	Weak transcription	Primary T cells from cord blood	blood
29	chr3:52331000-52343200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:52331200-52334200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:52331200-52335200	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:52331200-52342800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:52331400-52333800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:52331400-52336400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:52331600-52334600	Enhancers	Fetal Thymus	thymus
36	chr3:52331600-52335200	Enhancers	Stomach Mucosa	stomach
37	chr3:52331800-52334000	Weak transcription	HSMM	muscle
38	chr3:52331800-52335600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:52332000-52334200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:52332000-52335200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr3:52332000-52335200	Enhancers	Placenta	Placenta
42	chr3:52332200-52333800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr3:52332200-52333800	Weak transcription	HSMMtube	muscle
44	chr3:52332200-52334000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:52332200-52334000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:52332200-52335200	Enhancers	Lung	lung
47	chr3:52332400-52334400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:52332400-52334600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:52332400-52335200	Enhancers	Right Ventricle	heart
50	chr3:52332600-52334400	Active TSS	H9 Cell Line	embryonic stem cell

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