Variant report

Variant	rs17015217
Chromosome Location	chr1:209966629-209966630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209957348..209959526-chr1:209965730..209967837,2	K562	blood:
2	chr1:209957266..209960368-chr1:209964452..209967778,3	MCF-7	breast:
3	chr1:209955602..209959674-chr1:209962858..209967873,6	MCF-7	breast:
4	chr1:209963821..209966213-chr1:209966523..209968163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117595	Chromatin interaction
ENSG00000162757	Chromatin interaction

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

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

rs_ID	r²[population]
rs10489343	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779514	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779515	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863789	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1109430	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119345	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11119346	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119347	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119348	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12058100	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12064398	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12069187	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12075674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12080691	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12081405	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12083685	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12405750	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566152	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1856161	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2069068	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076149	0.84[AMR][1000 genomes]
rs2076151	0.81[AMR][1000 genomes]
rs2142860	0.84[AMR][1000 genomes]
rs2235370	0.94[AMR][1000 genomes]
rs2235371	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294406	0.84[AMR][1000 genomes]
rs3753517	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274836	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4140636	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4329516	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4844491	0.81[AMR][1000 genomes]
rs4844494	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844496	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][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

No data

Chromatin state (count:47 , 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	chr1:209958600-209967000	Genic enhancers	NHEK	skin
8	chr1:209958600-209971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:209958600-209972000	Weak transcription	Fetal Kidney	kidney
10	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
11	chr1:209960800-209969000	Strong transcription	Placenta	Placenta
12	chr1:209961000-209974600	Weak transcription	Right Atrium	heart
13	chr1:209961600-209974600	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr1:209962000-209972600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:209962200-209977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:209963600-209967000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:209964200-209976000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:209964200-209977800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:209964200-209978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:209964400-209968000	Weak transcription	HUVEC	blood vessel
22	chr1:209964400-209978200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:209964600-209967600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:209964600-209968000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:209964600-209971600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:209965200-209975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:209965600-209969600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:209965800-209968400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:209965800-209970600	Strong transcription	Liver	Liver
30	chr1:209965800-209974600	Weak transcription	Small Intestine	intestine
31	chr1:209966000-209968000	Weak transcription	Fetal Intestine Small	intestine
32	chr1:209966000-209968400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:209966000-209968400	Weak transcription	Esophagus	oesophagus
34	chr1:209966000-209968400	Weak transcription	Gastric	stomach
35	chr1:209966000-209969400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:209966000-209973000	Weak transcription	Left Ventricle	heart
37	chr1:209966000-209976200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:209966000-209978000	Weak transcription	Colonic Mucosa	Colon
39	chr1:209966000-209978400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:209966200-209967000	Weak transcription	Pancreas	Pancrea
41	chr1:209966200-209968600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:209966200-209970800	Weak transcription	Stomach Mucosa	stomach
43	chr1:209966200-209974600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr1:209966400-209971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:209966400-209971200	Strong transcription	HMEC	breast
46	chr1:209966600-209968400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:209966600-209968600	Strong transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links