Variant report

Variant	rs601436
Chromosome Location	chr15:41171132-41171133
allele	A/G
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	chr15:41170967-41171379	Hela-S3	cervix:	n/a	n/a
2	CREB1	chr15:41170923-41171454	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:41171057-41171337	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr15:41170996-41171397	Hela-S3	cervix:	n/a	chr15:41171179-41171189 chr15:41171178-41171189 chr15:41171179-41171188 chr15:41171180-41171189
5	SPI1	chr15:41171029-41171349	GM12891	blood:	n/a	n/a
6	RELA	chr15:41171001-41171395	GM18505	blood:	n/a	n/a
7	CREB1	chr15:41170922-41171377	GM12878	blood:	n/a	n/a
8	STAT3	chr15:41171020-41171397	Hela-S3	cervix:	n/a	chr15:41171180-41171189 chr15:41171155-41171163 chr15:41171238-41171249
9	FOS	chr15:41170764-41171482	MCF10A-Er-Src	breast:	n/a	chr15:41171179-41171189 chr15:41171178-41171189 chr15:41171179-41171188 chr15:41171180-41171189
10	JUND	chr15:41171024-41171363	HepG2	liver:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189 chr15:41171178-41171189
11	MTA3	chr15:41170780-41171453	GM12878	blood:	n/a	n/a
12	FOS	chr15:41170993-41171380	MCF10A-Er-Src	breast:	n/a	chr15:41171179-41171189 chr15:41171178-41171189 chr15:41171179-41171188 chr15:41171180-41171189
13	RUNX3	chr15:41170982-41171309	GM12878	blood:	n/a	n/a
14	TCF7L2	chr15:41170735-41171236	Hela-S3	cervix:	n/a	chr15:41171179-41171188 chr15:41171180-41171189
15	EBF1	chr15:41170964-41171402	GM12878	blood:	n/a	n/a
16	TBL1XR1	chr15:41171068-41171367	GM12878	blood:	n/a	n/a
17	MYC	chr15:41171121-41171477	MCF10A-Er-Src	breast:	n/a	chr15:41171179-41171188
18	ATF3	chr15:41171020-41171303	K562	blood:	n/a	n/a
19	EP300	chr15:41171051-41171335	GM12878	blood:	n/a	chr15:41171179-41171188
20	JUND	chr15:41170725-41171402	Hela-S3	cervix:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189 chr15:41171178-41171189
21	FOSL2	chr15:41170903-41171335	MCF-7	breast:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189
22	NFIC	chr15:41170917-41171512	GM12878	blood:	n/a	n/a
23	RELA	chr15:41170998-41171393	GM18951	blood:	n/a	n/a
24	RCOR1	chr15:41171117-41171268	K562	blood:	n/a	n/a
25	RELA	chr15:41171047-41171416	GM19099	blood:	n/a	n/a
26	JUND	chr15:41171028-41171321	H1-hESC	embryonic stem cell:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189 chr15:41171178-41171189
27	FOSL2	chr15:41171009-41171373	A549	lung:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189
28	STAT3	chr15:41170976-41171479	MCF10A-Er-Src	breast:	n/a	chr15:41171180-41171189 chr15:41171155-41171163 chr15:41171238-41171249
29	EP300	chr15:41170986-41171352	GM12878	blood:	n/a	chr15:41171179-41171188
30	RUNX3	chr15:41170897-41171375	GM12878	blood:	n/a	n/a
31	FOSL1	chr15:41170869-41171491	HCT-116	colon:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189
32	STAT3	chr15:41170996-41171490	MCF10A-Er-Src	breast:	n/a	chr15:41171180-41171189 chr15:41171155-41171163 chr15:41171238-41171249
33	PML	chr15:41170799-41171406	GM12878	blood:	n/a	chr15:41171178-41171187
34	JUND	chr15:41171080-41171285	H1-hESC	embryonic stem cell:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189 chr15:41171178-41171189
35	FOS	chr15:41170775-41171460	MCF10A-Er-Src	breast:	n/a	chr15:41171179-41171189 chr15:41171178-41171189 chr15:41171179-41171188 chr15:41171180-41171189
36	RFX5	chr15:41170752-41171480	Hela-S3	cervix:	n/a	n/a
37	STAT3	chr15:41170943-41171474	MCF10A-Er-Src	breast:	n/a	chr15:41171180-41171189 chr15:41171155-41171163 chr15:41171238-41171249
38	USF2	chr15:41171055-41171329	Hela-S3	cervix:	n/a	n/a
39	JUND	chr15:41171009-41171374	K562	blood:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189 chr15:41171178-41171189
40	WRNIP1	chr15:41170990-41171282	GM12878	blood:	n/a	n/a
41	CHD2	chr15:41171005-41171346	GM12878	blood:	n/a	n/a
42	STAT5A	chr15:41171039-41171283	GM12878	blood:	n/a	chr15:41171180-41171189 chr15:41171155-41171163
43	MAX	chr15:41171117-41171313	GM12878	blood:	n/a	chr15:41171179-41171188
44	YY1	chr15:41171091-41171299	GM12878	blood:	n/a	n/a
45	JUN	chr15:41170941-41171528	K562	blood:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189
46	RFX5	chr15:41170916-41171359	IMR90	lung:	n/a	n/a
47	RFX5	chr15:41170898-41171431	GM12878	blood:	n/a	n/a
48	POLR2A	chr15:41171099-41171258	Hela-S3	cervix:	n/a	n/a
49	BHLHE40	chr15:41171051-41171370	GM12878	blood:	n/a	n/a
50	FOSL2	chr15:41170945-41171434	MCF-7	breast:	n/a	chr15:41171179-41171189 chr15:41171179-41171188 chr15:41171180-41171189

No.	Distal block	Cell Line	Cell type
1	chr15:41164548..41167013-chr15:41169741..41172530,3	K562	blood:
2	chr15:41136155..41137886-chr15:41171120..41173235,2	MCF-7	breast:
3	chr15:41149992..41152598-chr15:41170919..41172722,2	K562	blood:
4	chr15:41162670..41167834-chr15:41168515..41173358,14	MCF-7	breast:
5	chr15:41168787..41171767-chr15:41172329..41175308,2	MCF-7	breast:
6	chr15:41164565..41167944-chr15:41168228..41172256,5	K562	blood:
7	chr15:41148133..41159834-chr15:41169228..41175193,12	MCF-7	breast:

Variant related genes	Relation type
RHOV	TF binding region
ENSG00000264256	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000261183	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11070298	0.90[EUR][1000 genomes]
rs11070299	0.89[EUR][1000 genomes]
rs11070301	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070304	0.92[EUR][1000 genomes]
rs11635602	0.86[ASN][1000 genomes]
rs11856227	1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs12101494	0.89[EUR][1000 genomes]
rs12148523	0.87[EUR][1000 genomes]
rs12903603	0.84[EUR][1000 genomes]
rs12916961	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16971157	1.00[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs16971177	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs16971186	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs16971188	0.85[CHB][hapmap]
rs1814568	0.82[CHB][hapmap]
rs1814692	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279578	1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs2412571	0.90[EUR][1000 genomes]
rs2445490	0.81[ASN][1000 genomes]
rs28444382	0.82[EUR][1000 genomes]
rs3100810	0.86[ASN][1000 genomes]
rs3743036	0.86[CHB][hapmap]
rs4244581	0.83[EUR][1000 genomes]
rs4384588	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4923885	0.89[EUR][1000 genomes]
rs4923886	1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs4923887	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4924509	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs595559	0.86[CHB][hapmap]
rs601696	0.86[ASN][1000 genomes]
rs615987	0.86[ASN][1000 genomes]
rs616606	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617377	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs618892	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625058	1.00[CEU][hapmap]
rs675262	0.86[CHB][hapmap];0.94[CHD][hapmap]
rs677273	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs682130	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs687949	0.86[ASN][1000 genomes]
rs690365	0.86[CHB][hapmap];0.94[CHD][hapmap]
rs694213	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs7172280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7175294	0.80[EUR][1000 genomes]
rs8024861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025867	0.85[CHB][hapmap]
rs8028660	0.88[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs8042095	0.90[EUR][1000 genomes]
rs880428	0.81[CHD][hapmap];1.00[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs601436	SPINT1	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41166800-41172400	Enhancers	Placenta	Placenta
2	chr15:41167000-41171200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:41168400-41171600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:41168600-41171200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:41170000-41171400	Flanking Active TSS	Hela-S3	cervix
6	chr15:41170000-41172200	Enhancers	GM12878-XiMat	blood
7	chr15:41170000-41172200	Enhancers	NHEK	skin
8	chr15:41170400-41171200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr15:41170400-41172200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:41170600-41171200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:41170600-41171600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:41170600-41171800	Enhancers	HMEC	breast
13	chr15:41170800-41171200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr15:41170800-41171800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr15:41170800-41172000	Enhancers	Stomach Mucosa	stomach
16	chr15:41170800-41172200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:41170800-41172600	Enhancers	K562	blood
18	chr15:41171000-41171200	Enhancers	A549	lung
19	chr15:41171000-41171400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr15:41171000-41171400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr15:41171000-41171400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:41171000-41171400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr15:41171000-41171600	Enhancers	Fetal Thymus	thymus
24	chr15:41171000-41172000	Enhancers	Duodenum Mucosa	Duodenum

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