Variant report

Variant	rs10495217
Chromosome Location	chr1:223905020-223905021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223903451..223905300-chr1:223920938..223923297,2	MCF-7	breast:
2	chr1:223903418..223905687-chr1:223928822..223931791,2	MCF-7	breast:
3	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
4	chr1:223904423..223906015-chr1:223946207..223948782,2	K562	blood:
5	chr1:223904247..223905976-chr1:223916920..223919197,2	MCF-7	breast:
6	chr1:223895202..223897591-chr1:223904463..223906328,2	K562	blood:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10465524	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10495215	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10503144	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12059770	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12066704	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs12069561	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs12080250	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12088254	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap]
rs1222138	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs1222141	0.85[CEU][hapmap]
rs12563637	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs12565967	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12566817	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12568612	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1629836	1.00[CEU][hapmap]
rs16841190	1.00[JPT][hapmap]
rs16842162	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16842257	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16842326	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16842343	1.00[JPT][hapmap]
rs17556570	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17557288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17557525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17557623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs28370026	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370031	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370032	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370043	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3738373	0.85[CEU][hapmap]
rs3738374	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs4653522	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4993742	0.82[CEU][hapmap]
rs61823964	0.87[EUR][1000 genomes]
rs61823979	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6671245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678365	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6683052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6685557	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6691315	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6693372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693884	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694960	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6696053	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6700366	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6703104	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7331	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs751609	0.85[CEU][hapmap]
rs7530328	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7533551	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7535882	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7549063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv437346	chr1:223903781-223905532	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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 target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223900800-223906000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:223901000-223905200	Enhancers	Spleen	Spleen
3	chr1:223901000-223905800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:223901200-223905400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:223901400-223905600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:223901400-223907600	Transcr. at gene 5' and 3'	A549	lung
7	chr1:223901600-223905200	Transcr. at gene 5' and 3'	NHEK	skin
8	chr1:223901600-223905800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:223901600-223906200	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:223901600-223906400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:223901800-223905200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:223901800-223905600	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr1:223901800-223905800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:223901800-223906200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:223902200-223905200	Genic enhancers	Fetal Muscle Leg	muscle
16	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:223902400-223905800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:223902400-223906200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:223902400-223906600	Enhancers	Fetal Thymus	thymus
20	chr1:223902600-223905200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr1:223902600-223905400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr1:223902600-223906000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:223903000-223905800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:223903000-223906000	Enhancers	Primary B cells from cord blood	blood
26	chr1:223903000-223907800	Weak transcription	Liver	Liver
27	chr1:223903200-223906400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:223903200-223907200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:223903400-223905200	Weak transcription	Pancreas	Pancrea
31	chr1:223903400-223906200	Strong transcription	Fetal Kidney	kidney
32	chr1:223903400-223907400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
33	chr1:223903400-223908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:223903400-223908800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:223903600-223905200	Genic enhancers	Esophagus	oesophagus
36	chr1:223903600-223909400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:223903600-223911800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:223904000-223905200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr1:223904000-223909000	Genic enhancers	Hela-S3	cervix
41	chr1:223904000-223910000	Genic enhancers	Osteobl	bone
42	chr1:223904200-223905200	Weak transcription	Brain Germinal Matrix	brain
43	chr1:223904200-223906800	Strong transcription	Fetal Lung	lung
44	chr1:223904200-223909800	Genic enhancers	NH-A	brain
45	chr1:223904400-223905200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:223904400-223905200	Weak transcription	Aorta	Aorta
47	chr1:223904400-223905200	Weak transcription	Left Ventricle	heart
48	chr1:223904400-223905400	Weak transcription	Ovary	ovary
49	chr1:223904400-223906000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:223904400-223906000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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