Variant report

Variant	rs6502467
Chromosome Location	chr17:15608387-15608388
allele	G/T
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	chr17:15607701-15608466	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr17:15607704-15608404	GM12878	blood:	n/a	n/a
3	POU2F2	chr17:15607710-15608409	GM12878	blood:	n/a	n/a
4	POLR2A	chr17:15608287-15608537	A549	lung:	n/a	n/a
5	POLR2A	chr17:15607654-15608422	GM12892	blood:	n/a	n/a
6	POLR2A	chr17:15608127-15608608	MCF-7	breast:	n/a	n/a
7	POLR2A	chr17:15607292-15608423	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:15607710-15608438	GM12892	blood:	n/a	n/a
9	POLR2A	chr17:15607799-15608454	Hela-S3	cervix:	n/a	n/a
10	HEY1	chr17:15607818-15608387	K562	blood:	n/a	chr17:15608318-15608333
11	POLR2A	chr17:15607719-15608436	GM12878	blood:	n/a	n/a
12	POLR2A	chr17:15607835-15608454	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr17:15608220-15608593	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr17:15608311-15608399	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:15607453-15608434	GM12892	blood:	n/a	n/a
16	POLR2A	chr17:15607781-15608410	GM12891	blood:	n/a	n/a
17	TAF1	chr17:15608068-15608404	HepG2	liver:	n/a	n/a
18	POLR2A	chr17:15607471-15608403	PFSK-1	brain:	n/a	n/a
19	POU2F2	chr17:15608198-15608439	GM12878	blood:	n/a	n/a
20	POLR2A	chr17:15607719-15608394	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr17:15608141-15608460	ProgFib	skin:	n/a	n/a
22	TCF3	chr17:15608138-15608400	GM12878	blood:	n/a	n/a
23	POLR2A	chr17:15608171-15608578	HUVEC	blood vessel:	n/a	n/a
24	TAF1	chr17:15608129-15608392	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr17:15607594-15608393	GM12891	blood:	n/a	n/a
26	POLR2A	chr17:15608021-15608539	HepG2	liver:	n/a	n/a
27	TAF1	chr17:15608138-15608406	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr17:15607792-15608615	K562	blood:	n/a	n/a
29	POLR2A	chr17:15608009-15608621	MCF-7	breast:	n/a	n/a
30	POLR2A	chr17:15607693-15608413	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr17:15607455-15608409	A549	lung:	n/a	n/a
32	POLR2A	chr17:15608003-15608599	Gliobla	brain:	n/a	n/a
33	POLR2A	chr17:15608300-15608516	MCF-7	breast:	n/a	n/a
34	POLR2A	chr17:15607644-15608393	A549	lung:	n/a	n/a
35	HEY1	chr17:15607418-15608400	K562	blood:	n/a	chr17:15608318-15608333
36	POLR2A	chr17:15607313-15608690	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr17:15607769-15608392	A549	lung:	n/a	n/a
38	POLR2A	chr17:15608239-15608388	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr17:15608290-15608494	H1-hESC	embryonic stem cell:	n/a	n/a
40	HEY1	chr17:15608140-15608498	HepG2	liver:	n/a	chr17:15608318-15608333

Variant related genes	Relation type
UBE2SP1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2601951	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2654397	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3760301	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55748835	0.82[ASN][1000 genomes]
rs8075077	0.81[EUR][1000 genomes]
rs9890181	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers 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	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv457695	chr17:15447364-15611495	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv574462	chr17:15447364-15611495	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
7	nsv520426	chr17:15554561-15647723	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv962262	chr17:15601321-15609621	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv515999	chr17:15608194-15611495	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
12	nsv827899	chr17:15608221-15609388	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6502467	ZNF286A	Cis_1M	lymphoblastoid	RTeQTL
rs6502467	ZNF286A	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15603200-15609200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:15603400-15608400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr17:15603400-15608400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:15603400-15608600	Weak transcription	Liver	Liver
5	chr17:15603400-15608600	Weak transcription	NHDF-Ad	bronchial
6	chr17:15603400-15608800	Weak transcription	Primary T cells from cord blood	blood
7	chr17:15603400-15609000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr17:15603400-15609000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:15603400-15609000	Weak transcription	Placenta	Placenta
10	chr17:15603400-15609200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr17:15603400-15609200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:15603400-15609200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr17:15603400-15609200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr17:15603400-15609200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:15603400-15609200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr17:15603400-15609200	Weak transcription	Fetal Kidney	kidney
17	chr17:15603400-15609200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr17:15603400-15609400	Weak transcription	Brain Anterior Caudate	brain
19	chr17:15603400-15609400	Weak transcription	Brain Substantia Nigra	brain
20	chr17:15603400-15609400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr17:15603400-15609600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr17:15603400-15609600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr17:15603400-15609600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr17:15603400-15609600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:15603400-15609600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr17:15603400-15609600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr17:15603400-15609600	Weak transcription	Thymus	Thymus
28	chr17:15603400-15609600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr17:15603400-15609800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr17:15603400-15609800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr17:15603400-15610200	Weak transcription	Aorta	Aorta
32	chr17:15603400-15610200	Weak transcription	Left Ventricle	heart
33	chr17:15603400-15610200	Weak transcription	Lung	lung
34	chr17:15603400-15610400	Weak transcription	Gastric	stomach
35	chr17:15603400-15610800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:15603400-15610800	Weak transcription	Adipose Nuclei	Adipose
37	chr17:15603400-15610800	Weak transcription	Psoas Muscle	Psoas
38	chr17:15603400-15610800	Weak transcription	NHLF	lung
39	chr17:15603400-15611000	Weak transcription	Brain Angular Gyrus	brain
40	chr17:15603400-15611000	Weak transcription	Right Ventricle	heart
41	chr17:15603400-15611600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr17:15603400-15612000	Weak transcription	Colon Smooth Muscle	Colon
43	chr17:15603400-15616400	Weak transcription	Pancreas	Pancrea
44	chr17:15603600-15609200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr17:15603600-15611000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr17:15603600-15619200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr17:15603800-15608400	Weak transcription	Fetal Intestine Small	intestine
48	chr17:15603800-15609200	Weak transcription	Brain Hippocampus Middle	brain
49	chr17:15603800-15609400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr17:15604000-15608400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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