Variant report

Variant	rs6779820
Chromosome Location	chr3:191046793-191046794
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:212)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:212 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:191046697-191047355	GM12878	blood:	n/a	n/a
2	SMC3	chr3:191046584-191047421	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:191046640-191047740	GM12878	blood:	n/a	n/a
4	BHLHE40	chr3:191046338-191047425	K562	blood:	n/a	chr3:191047106-191047122
5	STAT5A	chr3:191046490-191047404	GM12878	blood:	n/a	chr3:191047112-191047124
6	TAF1	chr3:191046786-191048115	ECC-1	luminal epithelium:	n/a	n/a
7	MTA3	chr3:191046498-191047642	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:191046161-191048563	GM19193	blood:	n/a	n/a
9	REST	chr3:191046768-191047338	PFSK-1	brain:	n/a	chr3:191047114-191047127
10	POLR2A	chr3:191046702-191048304	GM15510	blood:	n/a	n/a
11	FOS	chr3:191046513-191046818	MCF10A-Er-Src	breast:	n/a	chr3:191046637-191046648
12	TCF12	chr3:191046780-191047377	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr3:191046768-191048822	Hela-S3	cervix:	n/a	n/a
14	MAX	chr3:191046631-191048247	HepG2	liver:	n/a	n/a
15	ZNF384	chr3:191046734-191047240	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:191046759-191047417	K562	blood:	n/a	n/a
17	ZBTB7A	chr3:191046684-191048113	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr3:191045952-191047725	PFSK-1	brain:	n/a	n/a
19	MAFK	chr3:191046494-191046899	K562	blood:	n/a	n/a
20	EP300	chr3:191046362-191047392	K562	blood:	n/a	n/a
21	POLR2A	chr3:191046659-191047471	HCT-116	colon:	n/a	n/a
22	POLR2A	chr3:191046549-191048828	HUVEC	blood vessel:	n/a	n/a
23	RELA	chr3:191046517-191048835	GM18951	blood:	n/a	n/a
24	BHLHE40	chr3:191046462-191047422	GM12878	blood:	n/a	chr3:191047106-191047122
25	HA-E2F1	chr3:191046077-191048374	MCF-7	breast:	n/a	chr3:191048046-191048058
26	FOXA2	chr3:191046777-191047388	A549	lung:	n/a	n/a
27	POLR2A	chr3:191046404-191047614	K562	blood:	n/a	n/a
28	ELK1	chr3:191046785-191047343	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:191046439-191048127	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:191046775-191047302	GM12892	blood:	n/a	n/a
31	MAFK	chr3:191046695-191047491	Hela-S3	cervix:	n/a	n/a
32	ZNF143	chr3:191046783-191047465	H1-hESC	embryonic stem cell:	n/a	n/a
33	ELF1	chr3:191046604-191047502	HCT-116	colon:	n/a	chr3:191047181-191047194
34	SIN3AK20	chr3:191046448-191047420	PFSK-1	brain:	n/a	n/a
35	RFX5	chr3:191046576-191049678	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr3:191046684-191047478	SK-N-MC	brain:	n/a	n/a
37	RUNX3	chr3:191046367-191047463	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:191046728-191047353	GM12891	blood:	n/a	n/a
39	KAP1	chr3:191046053-191047043	U2OS	brain:	n/a	n/a
40	MAX	chr3:191046773-191047407	SK-N-SH	brain:	n/a	n/a
41	MYBL2	chr3:191046744-191047454	HepG2	liver:	n/a	n/a
42	HCFC1	chr3:191046494-191047943	K562	blood:	n/a	n/a
43	POLR2A	chr3:191046555-191047599	HepG2	liver:	n/a	n/a
44	TBL1XR1	chr3:191046370-191047299	K562	blood:	n/a	n/a
45	NR2F2	chr3:191046725-191047887	MCF-7	breast:	n/a	n/a
46	NR2F2	chr3:191045930-191047215	K562	blood:	n/a	n/a
47	SIN3A	chr3:191046619-191048409	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr3:191046766-191047552	PANC-1	pancreas:	n/a	n/a
49	POU2F2	chr3:191046668-191047400	GM12878	blood:	n/a	n/a
50	RCOR1	chr3:191046379-191049021	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:190999845..191001643-chr3:191046703..191048798,2	MCF-7	breast:
2	chr3:191032916..191035495-chr3:191046200..191047748,2	MCF-7	breast:
3	chr16:8962585..8963523-chr3:191046236..191047148,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GMNC-5	chr3:191046593-191047101	NONHSAT093964

No data

Variant related genes	Relation type
CCDC50	TF binding region
ENSG00000153048	Chromatin interaction
ENSG00000261481	Chromatin interaction
ENSG00000188958	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10937477	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1347400	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1465737	0.87[ASN][1000 genomes]
rs1473866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs150506	0.87[ASN][1000 genomes]
rs159488	0.91[ASN][1000 genomes]
rs159489	0.87[ASN][1000 genomes]
rs176820	0.82[CHB][hapmap]
rs186063	0.82[CHB][hapmap]
rs186066	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs188384	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs188385	0.83[ASN][1000 genomes]
rs192671	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs293797	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs293798	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs293800	0.85[ASN][1000 genomes]
rs293802	0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs293804	0.85[ASN][1000 genomes]
rs293805	0.81[ASN][1000 genomes]
rs293806	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs293808	0.87[ASN][1000 genomes]
rs293815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs293844	0.87[ASN][1000 genomes]
rs293846	0.87[ASN][1000 genomes]
rs293851	0.87[ASN][1000 genomes]
rs297396	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs366626	0.82[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs367747	0.85[ASN][1000 genomes]
rs368665	0.85[ASN][1000 genomes]
rs369174	0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs373035	0.87[ASN][1000 genomes]
rs381090	0.87[ASN][1000 genomes]
rs383075	0.83[ASN][1000 genomes]
rs390744	0.87[ASN][1000 genomes]
rs401465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs426466	0.87[ASN][1000 genomes]
rs432085	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs434556	0.85[ASN][1000 genomes]
rs437244	0.85[ASN][1000 genomes]
rs448133	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs448643	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4677630	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4677734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4677735	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs523270	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs525774	0.87[ASN][1000 genomes]
rs526785	0.87[ASN][1000 genomes]
rs529523	0.87[ASN][1000 genomes]
rs566548	0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs6953	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs697905	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs709142	0.87[ASN][1000 genomes]
rs9847278	0.98[ASN][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	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv878101	chr3:190891939-191059322	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1851611	chr3:191028147-191073560	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv4169	chr3:191036298-191063465	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv3325773	chr3:191046083-191048631	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv10370	chr3:191046223-191049560	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191046000-191046800	Enhancers	Spleen	Spleen
2	chr3:191046200-191046800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
3	chr3:191046200-191046800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:191046200-191046800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:191046200-191046800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
6	chr3:191046200-191046800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:191046200-191046800	Flanking Active TSS	Fetal Brain Female	brain
8	chr3:191046200-191046800	Flanking Active TSS	Fetal Kidney	kidney
9	chr3:191046200-191046800	Enhancers	Pancreas	Pancrea
10	chr3:191046200-191047000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:191046200-191047000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr3:191046200-191047000	Flanking Active TSS	Hela-S3	cervix
13	chr3:191046200-191049200	Active TSS	Brain Angular Gyrus	brain
14	chr3:191046200-191049800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:191046200-191049800	Active TSS	Stomach Smooth Muscle	stomach
16	chr3:191046400-191046800	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
17	chr3:191046400-191046800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:191046400-191046800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:191046400-191046800	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr3:191046400-191046800	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr3:191046400-191046800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:191046400-191046800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:191046400-191046800	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr3:191046400-191046800	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr3:191046400-191046800	Enhancers	Small Intestine	intestine
26	chr3:191046400-191046800	Flanking Active TSS	NHDF-Ad	bronchial
27	chr3:191046400-191046800	Flanking Active TSS	Osteobl	bone
28	chr3:191046400-191047000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:191046400-191047000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr3:191046400-191047000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
31	chr3:191046400-191047000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr3:191046400-191047000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:191046400-191047000	Flanking Active TSS	Liver	Liver
34	chr3:191046400-191047000	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr3:191046400-191047000	Flanking Active TSS	Fetal Brain Male	brain
36	chr3:191046400-191047000	Flanking Active TSS	Fetal Heart	heart
37	chr3:191046400-191047000	Flanking Active TSS	Fetal Lung	lung
38	chr3:191046400-191047000	Flanking Active TSS	GM12878-XiMat	blood
39	chr3:191046400-191047000	Flanking Active TSS	NH-A	brain
40	chr3:191046400-191047000	Flanking Active TSS	NHLF	lung
41	chr3:191046400-191048200	Active TSS	Rectal Smooth Muscle	rectum
42	chr3:191046400-191048400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:191046400-191048600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:191046400-191048600	Active TSS	Brain Cingulate Gyrus	brain
45	chr3:191046400-191048600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr3:191046400-191048800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:191046400-191049800	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr3:191046600-191046800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr3:191046600-191046800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:191046600-191046800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell

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