Variant report

Variant	rs2289126
Chromosome Location	chr15:31521665-31521666
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	RCOR1	chr15:31521420-31521796	Hela-S3	cervix:	n/a	n/a
2	RFX5	chr15:31521380-31521864	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:31521408-31521873	HepG2	liver:	n/a	n/a
4	PML	chr15:31521547-31521854	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:31521175-31522035	GM18526	blood:	n/a	n/a
6	NFIC	chr15:31521104-31521897	GM12878	blood:	n/a	n/a
7	HEY1	chr15:31521331-31521865	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:31520615-31522027	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:31521445-31521747	HCT-116	colon:	n/a	n/a
10	CUX1	chr15:31521384-31521861	GM12878	blood:	n/a	n/a
11	MXI1	chr15:31521168-31521907	GM12878	blood:	n/a	n/a
12	CTCF	chr15:31521580-31521730	GM06990	blood:	n/a	n/a
13	EBF1	chr15:31521285-31521923	GM12878	blood:	n/a	chr15:31521626-31521637 chr15:31521604-31521615
14	POLR2A	chr15:31521247-31521814	HepG2	liver:	n/a	n/a
15	POLR2A	chr15:31520347-31523698	GM19193	blood:	n/a	n/a
16	POLR2A	chr15:31521415-31521807	HepG2	liver:	n/a	n/a
17	STAT1	chr15:31521382-31521801	GM12878	blood:	n/a	chr15:31521501-31521513
18	POLR2A	chr15:31521361-31521835	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr15:31521433-31521737	GM12892	blood:	n/a	chr15:31521489-31521499 chr15:31521492-31521501 chr15:31521486-31521504 chr15:31521481-31521502
20	POLR2A	chr15:31521126-31523649	GM15510	blood:	n/a	n/a
21	POLR2A	chr15:31521211-31522017	GM12878	blood:	n/a	n/a
22	RELA	chr15:31521230-31521879	GM15510	blood:	n/a	n/a
23	RUNX3	chr15:31521057-31521941	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:31521509-31521738	HCT-116	colon:	n/a	n/a
25	POLR2A	chr15:31521396-31521851	HepG2	liver:	n/a	n/a
26	SIN3A	chr15:31521286-31521787	GM12878	blood:	n/a	chr15:31521353-31521362
27	TBP	chr15:31521295-31521937	GM12878	blood:	n/a	n/a
28	ZNF384	chr15:31521549-31521970	GM12878	blood:	n/a	n/a
29	ELK1	chr15:31521347-31521844	GM12878	blood:	n/a	n/a
30	CHD2	chr15:31521650-31521794	Hela-S3	cervix:	n/a	n/a
31	TAF1	chr15:31521492-31521834	GM12891	blood:	n/a	n/a
32	BCLAF1	chr15:31521261-31521857	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:31519807-31521967	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:31520064-31522040	GM12878	blood:	n/a	n/a
35	POU2F2	chr15:31521381-31521902	GM12891	blood:	n/a	chr15:31521503-31521515 chr15:31521497-31521509 chr15:31521500-31521512
36	POLR2A	chr15:31521324-31521968	GM10847	blood:	n/a	n/a
37	POLR2A	chr15:31519537-31523614	GM12878	blood:	n/a	n/a
38	HEY1	chr15:31521425-31521706	HepG2	liver:	n/a	n/a
39	PML	chr15:31521114-31521926	GM12878	blood:	n/a	n/a
40	EP300	chr15:31521279-31521858	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:31520857-31521865	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:31521372-31521867	HepG2	liver:	n/a	n/a
43	ZNF143	chr15:31521264-31521903	GM12878	blood:	n/a	n/a
44	CTCF	chr15:31521540-31521690	GM12871	blood:	n/a	n/a
45	CTCF	chr15:31521550-31521748	GM19239	blood:	n/a	n/a
46	RCOR1	chr15:31521575-31521700	HepG2	liver:	n/a	n/a
47	POLR2A	chr15:31519660-31523811	Raji	blood:	n/a	n/a
48	POLR2A	chr15:31521141-31521888	GM12878	blood:	n/a	n/a
49	ELF1	chr15:31521067-31521842	GM12878	blood:	n/a	n/a
50	TAF1	chr15:31521333-31521902	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31507734..31509504-chr15:31521434..31524217,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259772	TF binding region
ENSG00000259448	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17815893	0.83[CEU][hapmap]
rs2009358	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2061210	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061211	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304507	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28379600	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28392854	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28469347	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28605389	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28718174	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28826082	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4304986	0.81[EUR][1000 genomes]
rs4329885	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62037869	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62037871	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754612	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription 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 miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers 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	84 gene(s)	inside rSNPs	diseases
3	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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
9	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active 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 target site	33 gene(s)	inside rSNPs	diseases
10	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv903839	chr15:31495113-31576677	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
13	nsv977067	chr15:31509197-31523063	Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31516200-31522000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:31516800-31523000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:31516800-31525400	Weak transcription	Right Ventricle	heart
4	chr15:31518400-31540600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:31520000-31521800	Flanking Active TSS	Primary B cells from peripheral blood	blood
6	chr15:31520000-31521800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:31520000-31522000	Enhancers	Fetal Thymus	thymus
8	chr15:31520000-31524200	Enhancers	Thymus	Thymus
9	chr15:31520200-31521800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr15:31520200-31522400	Active TSS	GM12878-XiMat	blood
11	chr15:31520600-31521800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:31520600-31521800	Active TSS	Colonic Mucosa	Colon
13	chr15:31520800-31521800	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr15:31520800-31525200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:31520800-31533600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:31521200-31521800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr15:31521200-31521800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr15:31521200-31521800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:31521200-31521800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr15:31521200-31521800	Enhancers	Fetal Intestine Small	intestine
21	chr15:31521200-31521800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr15:31521200-31521800	Flanking Active TSS	Hela-S3	cervix
23	chr15:31521200-31523800	Enhancers	Esophagus	oesophagus
24	chr15:31521400-31521800	Enhancers	Fetal Heart	heart
25	chr15:31521400-31521800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr15:31521400-31521800	Bivalent Enhancer	Fetal Stomach	stomach
27	chr15:31521400-31521800	Enhancers	Lung	lung
28	chr15:31521400-31521800	Enhancers	Pancreas	Pancrea
29	chr15:31521400-31521800	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr15:31521400-31521800	Active TSS	A549	lung
31	chr15:31521400-31528600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:31521600-31521800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:31521600-31521800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:31521600-31521800	Enhancers	Duodenum Mucosa	Duodenum
35	chr15:31521600-31521800	Flanking Active TSS	Gastric	stomach
36	chr15:31521600-31521800	Enhancers	Spleen	Spleen
37	chr15:31521600-31521800	Flanking Active TSS	HepG2	liver
38	chr15:31521600-31522000	Enhancers	Stomach Mucosa	stomach
39	chr15:31521600-31526400	Weak transcription	Left Ventricle	heart

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