Variant report

Variant	rs3093977
Chromosome Location	chr6:31500226-31500227
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:59)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:59 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31496675-31504805	K562	blood:	n/a	n/a
2	HEY1	chr6:31500192-31500676	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:31499848-31500419	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:31498081-31500681	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:31500017-31501405	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:31499465-31500774	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:31499380-31504726	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:31499604-31500679	HCT-116	colon:	n/a	n/a
9	POLR2A	chr6:31499883-31502108	MCF-7	breast:	n/a	n/a
10	POLR2A	chr6:31499814-31500906	HL-60	blood:	n/a	n/a
11	POLR2A	chr6:31499214-31503706	GM12892	blood:	n/a	n/a
12	POLR2A	chr6:31499387-31504628	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:31499310-31504797	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:31500062-31500667	K562	blood:	n/a	n/a
15	POLR2A	chr6:31500209-31501277	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:31499446-31502569	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:31499961-31500445	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:31499963-31500705	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:31499446-31503904	GM12892	blood:	n/a	n/a
20	POLR2A	chr6:31499455-31504043	K562	blood:	n/a	n/a
21	PML	chr6:31499796-31501297	K562	blood:	n/a	n/a
22	POLR2A	chr6:31499783-31502961	GM12891	blood:	n/a	n/a
23	POLR2A	chr6:31499896-31501558	GM12891	blood:	n/a	n/a
24	POLR2A	chr6:31496062-31502245	HepG2	liver:	n/a	n/a
25	ZNF263	chr6:31500013-31500683	HEK293-T-REx	kidney:	n/a	n/a
26	POLR2A	chr6:31498087-31501722	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr6:31500188-31500892	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr6:31499786-31502279	HepG2	liver:	n/a	n/a
29	POLR2A	chr6:31498516-31501574	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:31498116-31504635	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr6:31496067-31504034	GM12892	blood:	n/a	n/a
32	POLR2A	chr6:31496071-31504008	K562	blood:	n/a	n/a
33	POLR2A	chr6:31498805-31501161	HL-60	blood:	n/a	n/a
34	POLR2A	chr6:31499439-31500856	H1-neurons	neurons:	n/a	n/a
35	POLR2A	chr6:31495864-31501453	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr6:31499571-31500708	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr6:31495656-31505050	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr6:31499972-31502283	HepG2	liver:	n/a	n/a
39	POLR2A	chr6:31499573-31501313	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr6:31499314-31501838	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr6:31496688-31504446	K562	blood:	n/a	n/a
42	POLR2A	chr6:31499900-31500691	GM12891	blood:	n/a	n/a
43	POLR2A	chr6:31496018-31504683	HepG2	liver:	n/a	n/a
44	POLR2A	chr6:31499543-31500719	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr6:31498291-31503214	A549	lung:	n/a	n/a
46	POLR2A	chr6:31496124-31504583	K562	blood:	n/a	n/a
47	POLR2A	chr6:31499961-31500346	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:31499316-31503114	GM12891	blood:	n/a	n/a
49	POLR2A	chr6:31499006-31501845	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr6:31496050-31504648	PFSK-1	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31461211..31463484-chr6:31498734..31500993,3	K562	blood:
2	chr6:31499897..31502152-chr6:31623744..31626169,2	K562	blood:
3	chr6:31459795..31462964-chr6:31499493..31502905,3	K562	blood:
4	chr6:31497072..31502351-chr6:31549039..31551366,5	K562	blood:
5	chr6:31499501..31502092-chr6:31587750..31590043,2	K562	blood:
6	chr6:30582838..30585806-chr6:31497369..31500539,3	K562	blood:
7	chr6:31499682..31501227-chr6:31540656..31543059,2	K562	blood:

No data

Variant related genes	Relation type
DDX39B	TF binding region
ENSG00000227198	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000227507	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1129640	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516393	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516394	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523502	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523508	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523510	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523511	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093948	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093950	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093976	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093978	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093979	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093980	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093981	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093983	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093984	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093985	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093986	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093990	0.83[EUR][1000 genomes]
rs3093995	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094001	0.88[EUR][1000 genomes]
rs3095235	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3115536	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3115537	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130054	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130056	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130057	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130058	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130638	0.93[EUR][1000 genomes]
rs3131628	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131629	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3131630	0.88[ASN][1000 genomes]
rs3131633	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3132458	0.87[EUR][1000 genomes]
rs3132461	0.87[EUR][1000 genomes]
rs9267293	0.85[EUR][1000 genomes]
rs9267485	0.88[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	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
4	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
5	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
6	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
7	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
8	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	378 gene(s)	inside rSNPs	diseases
9	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
10	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
11	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
12	nsv1018463	chr6:31337336-31525275	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
13	nsv538189	chr6:31337336-31525275	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
14	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
15	esv2757162	chr6:31353329-31542308	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
16	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
17	nsv432877	chr6:31412961-31528690	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
18	nsv884415	chr6:31458633-31501413	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
19	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
20	nsv470809	chr6:31496915-31544189	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 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	chr6:31467400-31506600	Weak transcription	Right Atrium	heart
2	chr6:31495800-31506200	Strong transcription	Thymus	Thymus
3	chr6:31496000-31502000	Weak transcription	Psoas Muscle	Psoas
4	chr6:31496000-31506200	Strong transcription	Fetal Brain Female	brain
5	chr6:31496200-31506400	Strong transcription	Fetal Stomach	stomach
6	chr6:31496200-31506800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:31496400-31503400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:31496400-31505600	Strong transcription	Fetal Thymus	thymus
9	chr6:31496400-31506000	Strong transcription	Brain Germinal Matrix	brain
10	chr6:31496800-31505800	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr6:31496800-31506400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:31496800-31506400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:31496800-31506400	Strong transcription	Gastric	stomach
14	chr6:31496800-31506600	Strong transcription	Brain Cingulate Gyrus	brain
15	chr6:31496800-31507800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:31497000-31502200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:31497000-31502600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr6:31497000-31506200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:31497000-31506400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:31497000-31506400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:31497200-31503200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:31497200-31503800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:31497200-31504800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:31497200-31505200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:31497200-31505600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:31497200-31506000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:31497200-31506000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:31497200-31506000	Strong transcription	Duodenum Mucosa	Duodenum
29	chr6:31497200-31506000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr6:31497200-31506400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:31497200-31506600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:31497200-31506600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr6:31497200-31506600	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr6:31497200-31506600	Strong transcription	A549	lung
35	chr6:31497200-31506600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr6:31497200-31506800	Strong transcription	Rectal Smooth Muscle	rectum
37	chr6:31497400-31503600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:31497400-31503800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:31497400-31504000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:31497400-31504800	Strong transcription	Brain Hippocampus Middle	brain
41	chr6:31497400-31505000	Strong transcription	Ovary	ovary
42	chr6:31497400-31505800	Strong transcription	Primary T cells from cord blood	blood
43	chr6:31497400-31506000	Strong transcription	Brain Anterior Caudate	brain
44	chr6:31497400-31506000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:31497400-31506200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:31497400-31506200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:31497400-31506200	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr6:31497400-31506200	Strong transcription	Colon Smooth Muscle	Colon
49	chr6:31497400-31506200	Strong transcription	HUVEC	blood vessel
50	chr6:31497400-31506200	Strong transcription	NH-A	brain

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