Variant report

Variant	rs6460159
Chromosome Location	chr7:64011423-64011424
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	POLR2A	chr7:64011419-64011536	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:64003492..64005655-chr7:64011278..64012854,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223974	TF binding region
ENSG00000173041	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10216120	1.00[ASN][1000 genomes]
rs10228666	0.86[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap]
rs10235312	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236450	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10238116	1.00[ASN][1000 genomes]
rs10238379	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10243731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10244141	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10248313	1.00[ASN][1000 genomes]
rs10248437	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256682	1.00[ASN][1000 genomes]
rs10258736	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10272999	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10279234	0.81[EUR][1000 genomes]
rs10949896	1.00[ASN][1000 genomes]
rs11766865	1.00[ASN][1000 genomes]
rs11768537	1.00[ASN][1000 genomes]
rs11773004	1.00[ASN][1000 genomes]
rs11973673	0.88[AFR][1000 genomes]
rs11974106	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11977336	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11979331	1.00[ASN][1000 genomes]
rs11979336	1.00[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12111607	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12698473	1.00[ASN][1000 genomes]
rs12698474	1.00[ASN][1000 genomes]
rs13229310	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13230924	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235345	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235710	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236187	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13237045	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13238250	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238743	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239925	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13242372	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243255	1.00[ASN][1000 genomes]
rs13243485	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246918	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247467	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127039	0.86[AFR][1000 genomes]
rs35654744	1.00[ASN][1000 genomes]
rs4448144	1.00[ASN][1000 genomes]
rs4582437	1.00[ASN][1000 genomes]
rs6460160	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952263	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957579	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958645	1.00[ASN][1000 genomes]
rs7357287	1.00[ASN][1000 genomes]
rs7456018	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802057	1.00[ASN][1000 genomes]
rs912161	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429759	chr7:63662150-64110550	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv429760	chr7:63687850-64110550	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv429761	chr7:63747498-64096138	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv2764000	chr7:63766980-64275251	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
7	nsv429762	chr7:63790450-64110550	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
9	nsv1031703	chr7:63839601-64225952	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
10	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
11	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv1023042	chr7:63956027-64116232	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv970855	chr7:63959414-64023731	ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv888271	chr7:63961212-64295884	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
15	nsv888273	chr7:63990100-64291622	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
16	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
17	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
19	nsv1021893	chr7:63995601-64155027	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
20	nsv538892	chr7:63995601-64155027	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6460159	ZNF117	cis	parietal	SCAN
rs6460159	ZNF680	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:63974400-64020000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr7:63978200-64022200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:63989200-64011600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:63989200-64022600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:63989400-64019400	Weak transcription	HUVEC	blood vessel
6	chr7:63989400-64023000	Weak transcription	Gastric	stomach
7	chr7:63994200-64022600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:63997400-64015000	Strong transcription	Dnd41	blood
9	chr7:63997600-64022600	Weak transcription	Fetal Kidney	kidney
10	chr7:63999800-64012400	Weak transcription	Fetal Intestine Large	intestine
11	chr7:64000400-64013600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:64000400-64022800	Weak transcription	Small Intestine	intestine
13	chr7:64002200-64012800	Weak transcription	NHLF	lung
14	chr7:64002400-64011600	Weak transcription	Aorta	Aorta
15	chr7:64002400-64011600	Weak transcription	Esophagus	oesophagus
16	chr7:64002400-64015200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:64002400-64018800	Weak transcription	Right Atrium	heart
18	chr7:64002400-64022600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr7:64002400-64022800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:64002600-64018000	Weak transcription	HSMMtube	muscle
21	chr7:64002600-64018800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr7:64002600-64019200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:64002600-64022400	Weak transcription	HMEC	breast
24	chr7:64002800-64015000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:64002800-64018400	Weak transcription	NH-A	brain
26	chr7:64002800-64018600	Weak transcription	HepG2	liver
27	chr7:64003000-64019200	Weak transcription	NHDF-Ad	bronchial
28	chr7:64003400-64013200	Weak transcription	Fetal Stomach	stomach
29	chr7:64003400-64021400	Weak transcription	Spleen	Spleen
30	chr7:64004000-64012400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr7:64004000-64021800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:64004200-64020600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr7:64004800-64011600	Weak transcription	Osteobl	bone
34	chr7:64004800-64022600	Weak transcription	Fetal Lung	lung
35	chr7:64005600-64018000	Weak transcription	Pancreas	Pancrea
36	chr7:64006200-64011600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:64006200-64012800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:64006200-64014800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr7:64006400-64012600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr7:64006400-64014000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr7:64006600-64012200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr7:64006600-64013000	Strong transcription	Primary T cells from cord blood	blood
43	chr7:64007000-64012200	ZNF genes & repeats	Primary B cells from cord blood	blood
44	chr7:64007000-64014000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:64007200-64013800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:64007400-64022600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:64007800-64012800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr7:64007800-64013800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr7:64007800-64021400	Weak transcription	NHEK	skin
50	chr7:64007800-64021600	Weak transcription	Placenta	Placenta

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