Variant report

Variant	rs2279578
Chromosome Location	chr15:41164344-41164345
allele	C/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	E2F4	chr15:41163755-41164370	GM12878	blood:	n/a	n/a
2	BCLAF1	chr15:41163836-41164466	GM12878	blood:	n/a	chr15:41164161-41164170
3	PAX5	chr15:41163833-41164361	GM12878	blood:	n/a	n/a
4	PML	chr15:41163827-41164404	GM12878	blood:	n/a	n/a
5	BCL3	chr15:41163919-41164737	GM12878	blood:	n/a	chr15:41164161-41164170
6	CUX1	chr15:41163858-41164704	GM12878	blood:	n/a	n/a
7	NRF1	chr15:41163918-41164842	GM12878	blood:	n/a	n/a
8	MAX	chr15:41163919-41164917	MCF-7	breast:	n/a	n/a
9	POLR2A	chr15:41163459-41164895	GM12892	blood:	n/a	n/a
10	NFIC	chr15:41163809-41164843	ECC-1	luminal epithelium:	n/a	n/a
11	MTA3	chr15:41163444-41165568	GM12878	blood:	n/a	n/a
12	MAZ	chr15:41163715-41164759	GM12878	blood:	n/a	n/a
13	EP300	chr15:41163914-41164827	GM12878	blood:	n/a	n/a
14	MAX	chr15:41163742-41164573	GM12878	blood:	n/a	n/a
15	ATF2	chr15:41163485-41164755	GM12878	blood:	n/a	n/a
16	FOXM1	chr15:41163708-41164602	GM12878	blood:	n/a	n/a
17	POLR2A	chr15:41161732-41164784	MCF10A-Er-Src	breast:	n/a	n/a
18	ZNF217	chr15:41164056-41164751	MCF-7	breast:	n/a	n/a
19	TBP	chr15:41163568-41164709	GM12878	blood:	n/a	n/a
20	POLR2A	chr15:41161738-41164928	MCF10A-Er-Src	breast:	n/a	n/a
21	ELF1	chr15:41163776-41164898	MCF-7	breast:	n/a	n/a
22	ELF1	chr15:41163905-41164796	GM12878	blood:	n/a	n/a
23	HDAC2	chr15:41163959-41164871	MCF-7	breast:	n/a	n/a
24	SP1	chr15:41163891-41164682	GM12878	blood:	n/a	chr15:41164101-41164110 chr15:41164270-41164284 chr15:41164270-41164280 chr15:41164100-41164112 chr15:41164102-41164111 chr15:41164100-41164112 chr15:41164271-41164280 chr15:41164097-41164111
25	EBF1	chr15:41163844-41164793	GM12878	blood:	n/a	chr15:41164195-41164206
26	YY1	chr15:41163927-41164368	GM12891	blood:	n/a	n/a
27	NR2F2	chr15:41163771-41164936	MCF-7	breast:	n/a	n/a
28	TBL1XR1	chr15:41163711-41164721	GM12878	blood:	n/a	n/a
29	WRNIP1	chr15:41163665-41165453	GM12878	blood:	n/a	n/a
30	ATF2	chr15:41163728-41164839	GM12878	blood:	n/a	n/a
31	NFATC1	chr15:41163394-41164726	GM12878	blood:	n/a	n/a
32	MAX	chr15:41163874-41164703	ECC-1	luminal epithelium:	n/a	n/a
33	JUND	chr15:41163587-41165283	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:41163650-41164854	GM12878	blood:	n/a	n/a
35	PAX5	chr15:41163900-41164706	GM12878	blood:	n/a	n/a
36	MTA3	chr15:41163402-41164638	GM12878	blood:	n/a	n/a
37	NFATC1	chr15:41163685-41164513	GM12878	blood:	n/a	n/a
38	STAT3	chr15:41164042-41164677	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:41162820-41166815	Hela-S3	cervix:	n/a	n/a
40	ESRRA	chr15:41163398-41165207	GM12878	blood:	n/a	chr15:41163834-41163844 chr15:41163694-41163710 chr15:41164051-41164061 chr15:41164051-41164061 chr15:41164051-41164063 chr15:41164050-41164063
41	EGR1	chr15:41163980-41164396	GM12878	blood:	n/a	chr15:41164266-41164279 chr15:41164179-41164193
42	TCF12	chr15:41163946-41164421	GM12878	blood:	n/a	chr15:41164155-41164162
43	ATF2	chr15:41163851-41164351	H1-hESC	embryonic stem cell:	n/a	n/a
44	PML	chr15:41163389-41164850	GM12878	blood:	n/a	n/a
45	FOSL2	chr15:41163962-41164699	MCF-7	breast:	n/a	n/a
46	NFIC	chr15:41163380-41164698	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:41163936-41164625	GM19099	blood:	n/a	n/a
48	PAX5	chr15:41164010-41164352	GM12878	blood:	n/a	n/a
49	POLR2A	chr15:41163392-41166601	GM12878	blood:	n/a	n/a
50	RAD21	chr15:41163967-41164384	GM12878	blood:	n/a	chr15:41164116-41164125

No.	Distal block	Cell Line	Cell type
1	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
2	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
3	chr15:41097815..41100803-chr15:41163733..41165563,2	K562	blood:
4	chr15:41116410..41118480-chr15:41162646..41165359,2	MCF-7	breast:
5	chr15:41164000..41165836-chr15:41190857..41193283,2	K562	blood:
6	chr15:41162876..41167684-chr15:41196844..41200482,5	MCF-7	breast:
7	chr15:41163900..41166288-chr15:41184445..41186416,4	MCF-7	breast:
8	chr15:41161907..41163827-chr15:41163924..41166003,2	K562	blood:

Variant related genes	Relation type
ENSG00000264256	TF binding region
ENSG00000166145	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000104129	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11070298	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11070299	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070304	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11070305	0.84[ASN][1000 genomes]
rs11855507	0.84[ASN][1000 genomes]
rs11856227	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12148515	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12148523	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12903603	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916961	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16971157	1.00[CEU][hapmap]
rs1814692	0.97[EUR][1000 genomes]
rs2412571	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28444382	0.88[EUR][1000 genomes]
rs4244581	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4384588	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923885	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923886	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923887	0.90[EUR][1000 genomes]
rs4924509	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4924510	0.90[ASN][1000 genomes]
rs601436	1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs616606	0.85[EUR][1000 genomes]
rs617377	0.90[EUR][1000 genomes]
rs618892	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs618916	0.87[EUR][1000 genomes]
rs625058	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs686038	0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs690507	0.88[EUR][1000 genomes]
rs7172280	1.00[CEU][hapmap]
rs8024861	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8024961	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs8028660	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8042095	0.85[EUR][1000 genomes]
rs9806683	0.91[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
2	chr15:41150000-41165600	Weak transcription	Spleen	Spleen
3	chr15:41151600-41165400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:41162600-41165000	Enhancers	Stomach Mucosa	stomach
5	chr15:41163000-41165800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:41163400-41165600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:41163600-41164800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr15:41163600-41164800	Enhancers	Fetal Intestine Small	intestine
9	chr15:41163600-41165000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:41163600-41165000	Flanking Active TSS	Hela-S3	cervix
11	chr15:41163600-41165800	Flanking Active TSS	GM12878-XiMat	blood
12	chr15:41163600-41166000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:41163800-41164400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr15:41163800-41164400	Enhancers	Fetal Thymus	thymus
15	chr15:41163800-41164600	Bivalent Enhancer	HepG2	liver
16	chr15:41163800-41164600	Flanking Active TSS	NHEK	skin
17	chr15:41163800-41165200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr15:41163800-41165200	Enhancers	Fetal Intestine Large	intestine
19	chr15:41163800-41165200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr15:41163800-41165400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr15:41163800-41165600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr15:41163800-41165600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:41163800-41165600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr15:41163800-41165800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:41163800-41165800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:41163800-41165800	Enhancers	Duodenum Mucosa	Duodenum
27	chr15:41163800-41165800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr15:41163800-41165800	Enhancers	HMEC	breast
29	chr15:41163800-41166200	Enhancers	Fetal Brain Male	brain
30	chr15:41164000-41164400	Enhancers	Colonic Mucosa	Colon
31	chr15:41164000-41164400	Weak transcription	Gastric	stomach
32	chr15:41164000-41164600	Enhancers	Fetal Brain Female	brain
33	chr15:41164000-41164600	Enhancers	A549	lung
34	chr15:41164000-41165400	Weak transcription	K562	blood
35	chr15:41164000-41165600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr15:41164200-41164400	Enhancers	Primary B cells from peripheral blood	blood
37	chr15:41164200-41164400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr15:41164200-41164400	Flanking Active TSS	Placenta	Placenta
39	chr15:41164200-41164600	Enhancers	Fetal Lung	lung
40	chr15:41164200-41164800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr15:41164200-41164800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr15:41164200-41164800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:41164200-41164800	Flanking Active TSS	Pancreas	Pancrea
44	chr15:41164200-41165800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr15:41164200-41166600	Active TSS	Esophagus	oesophagus

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