Variant report

Variant	rs11188939
Chromosome Location	chr10:98598059-98598060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98592318..98594800-chr10:98594886..98599322,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196233	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10437452	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11188937	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188940	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188947	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188954	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188955	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188956	1.00[ASW][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188959	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188967	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188971	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs11188978	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12241405	0.83[EUR][1000 genomes]
rs12242330	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243551	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244490	0.95[EUR][1000 genomes]
rs12246067	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12247344	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249381	0.87[ASW][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249427	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249891	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252424	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252435	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256424	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257413	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258355	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258469	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259265	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261278	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261881	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262784	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263331	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264014	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12265242	0.93[ASW][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266068	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266185	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12267926	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268216	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268272	0.93[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376965	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112175	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112190	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104785	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183449	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28439735	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505353	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28758432	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394767	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56867696	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57408003	0.86[ASN][1000 genomes]
rs57501540	0.83[EUR][1000 genomes]
rs57716318	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270704	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58376960	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59751908	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59938221	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59999388	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60576681	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61492214	0.91[EUR][1000 genomes]
rs6584101	0.95[EUR][1000 genomes]
rs7071211	0.93[ASW][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs7072273	1.00[ASW][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073150	0.85[CEU][hapmap]
rs7082316	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082838	0.87[ASW][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs7085822	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085851	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086875	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7090441	0.82[EUR][1000 genomes]
rs7090690	0.81[EUR][1000 genomes]
rs74153734	0.95[EUR][1000 genomes]
rs7893144	0.83[ASN][1000 genomes]
rs7893564	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894138	0.84[EUR][1000 genomes]
rs7894418	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895914	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7906294	0.84[EUR][1000 genomes]
rs7910221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918085	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920238	0.85[CEU][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs7921193	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921216	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921885	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv895910	chr10:98386483-98640994	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1053801	chr10:98506832-98610101	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	nsv825532	chr10:98567434-98618034	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98593800-98599600	Weak transcription	Lung	lung
2	chr10:98593800-98600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:98593800-98600600	Weak transcription	Esophagus	oesophagus
4	chr10:98593800-98601800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr10:98593800-98602800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:98593800-98606800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:98593800-98624200	Weak transcription	Colonic Mucosa	Colon
8	chr10:98594000-98604200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr10:98594200-98599200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:98594200-98600600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:98594200-98610200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:98594200-98610800	Weak transcription	Fetal Thymus	thymus
13	chr10:98594200-98639400	Weak transcription	Thymus	Thymus
14	chr10:98594400-98599600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:98594400-98618800	Weak transcription	Fetal Stomach	stomach
16	chr10:98594800-98599400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr10:98594800-98600400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:98595400-98599200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr10:98595600-98598600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr10:98595800-98600600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr10:98595800-98604200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:98595800-98610400	Weak transcription	Aorta	Aorta
23	chr10:98596000-98598600	Enhancers	Fetal Brain Female	brain
24	chr10:98596000-98599200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:98596000-98599800	Weak transcription	HMEC	breast
26	chr10:98596000-98600600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr10:98596000-98602600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:98596000-98610400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:98596200-98599000	Weak transcription	NHEK	skin
30	chr10:98596200-98599600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr10:98596200-98599800	Weak transcription	NHDF-Ad	bronchial
32	chr10:98596200-98600400	Weak transcription	NH-A	brain
33	chr10:98596200-98600600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr10:98596200-98602600	Weak transcription	Stomach Mucosa	stomach
35	chr10:98596200-98602800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr10:98596200-98610400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:98596200-98616200	Weak transcription	Brain Germinal Matrix	brain
38	chr10:98596400-98598200	Weak transcription	Brain Angular Gyrus	brain
39	chr10:98596400-98600000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr10:98596400-98600200	Weak transcription	Colon Smooth Muscle	Colon
41	chr10:98596400-98600400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr10:98596400-98600400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr10:98596400-98600400	Weak transcription	HUVEC	blood vessel
44	chr10:98596400-98600600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:98596400-98600600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr10:98596400-98600600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr10:98596400-98600600	Weak transcription	Small Intestine	intestine
48	chr10:98596400-98602200	Weak transcription	Primary T cells from cord blood	blood
49	chr10:98596400-98602400	Weak transcription	Placenta	Placenta
50	chr10:98596400-98602400	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links