Variant report

Variant	rs2235375
Chromosome Location	chr1:209965587-209965588
allele	C/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	FOS	chr1:209965312-209965645	MCF10A-Er-Src	breast:	n/a	chr1:209965460-209965471 chr1:209965458-209965467 chr1:209965458-209965468 chr1:209965457-209965469
2	FOS	chr1:209965292-209965629	MCF10A-Er-Src	breast:	n/a	chr1:209965460-209965471 chr1:209965458-209965467 chr1:209965458-209965468 chr1:209965457-209965469
3	FOS	chr1:209965312-209965626	MCF10A-Er-Src	breast:	n/a	chr1:209965460-209965471 chr1:209965458-209965467 chr1:209965458-209965468 chr1:209965457-209965469
4	STAT3	chr1:209965411-209965611	MCF10A-Er-Src	breast:	n/a	chr1:209965458-209965467 chr1:209965479-209965490 chr1:209965473-209965481

No.	Distal block	Cell Line	Cell type
1	chr1:209957266..209960368-chr1:209964452..209967778,3	MCF-7	breast:
2	chr1:209961943..209965694-chr1:209969094..209971510,3	K562	blood:
3	chr1:209955602..209959674-chr1:209962858..209967873,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232222	TF binding region
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1005287	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1044516	0.90[LWK][hapmap]
rs1160411	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11803382	0.94[YRI][hapmap]
rs12403599	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015218	0.93[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs17015224	0.81[AFR][1000 genomes]
rs17015226	0.89[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs17015250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2005982	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013162	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073485	0.96[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs2073486	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2179254	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235372	0.82[LWK][hapmap]
rs2235373	0.82[AFR][1000 genomes]
rs2236907	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236908	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236909	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294408	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357229	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753518	0.94[YRI][hapmap]
rs58637469	0.81[AFR][1000 genomes]
rs59043219	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6540560	0.95[YRI][hapmap]
rs6659549	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685182	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694552	0.81[AFR][1000 genomes]
rs742215	0.81[LWK][hapmap]
rs7545538	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545542	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550857	0.82[LWK][hapmap];0.95[YRI][hapmap]
rs7552506	0.87[ASW][hapmap];0.88[CEU][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs926346	0.82[AFR][1000 genomes]
rs926347	0.81[AFR][1000 genomes]
rs926348	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1067914	chr1:209955818-209972979	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2235375	IRF6	cis	cerebellum	SCAN
rs2235375	IKBKE	cis	parietal	SCAN
rs2235375	SYT14	cis	parietal	SCAN
rs2235375	REN	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958000-209971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209958400-209968600	Weak transcription	Lung	lung
4	chr1:209958400-209971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
6	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:209958600-209966200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:209958600-209966600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:209958600-209967000	Genic enhancers	NHEK	skin
10	chr1:209958600-209971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:209958600-209972000	Weak transcription	Fetal Kidney	kidney
12	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
13	chr1:209959600-209966000	Genic enhancers	Fetal Intestine Small	intestine
14	chr1:209960800-209969000	Strong transcription	Placenta	Placenta
15	chr1:209961000-209974600	Weak transcription	Right Atrium	heart
16	chr1:209961400-209966000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:209961400-209966000	Genic enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:209961600-209974600	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr1:209962000-209966200	Strong transcription	Pancreas	Pancrea
20	chr1:209962000-209972600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:209962200-209977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:209962400-209965600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:209962400-209965800	Genic enhancers	Liver	Liver
24	chr1:209963000-209966600	Genic enhancers	Fetal Intestine Large	intestine
25	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:209963600-209966000	Genic enhancers	Gastric	stomach
27	chr1:209963600-209967000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:209963800-209966400	Genic enhancers	HMEC	breast
29	chr1:209964000-209966200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:209964200-209966000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:209964200-209976000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:209964200-209977800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:209964200-209978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:209964400-209966000	Genic enhancers	Duodenum Mucosa	Duodenum
35	chr1:209964400-209968000	Weak transcription	HUVEC	blood vessel
36	chr1:209964400-209978200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:209964600-209967600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:209964600-209968000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:209964600-209971600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:209965000-209965800	Enhancers	Small Intestine	intestine
41	chr1:209965000-209966000	Enhancers	Colonic Mucosa	Colon
42	chr1:209965000-209966000	Genic enhancers	Esophagus	oesophagus
43	chr1:209965000-209966400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:209965200-209965600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:209965200-209966000	Strong transcription	Left Ventricle	heart
46	chr1:209965200-209966000	Genic enhancers	Rectal Mucosa Donor 29	rectum
47	chr1:209965200-209966200	Enhancers	Stomach Mucosa	stomach
48	chr1:209965200-209975400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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