Variant report

Variant	rs11169005
Chromosome Location	chr12:49811311-49811312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49809234..49812478-chr12:49813344..49815493,3	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10160947	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10161131	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10783314	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875955	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875958	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11168981	1.00[LWK][hapmap]
rs11169008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169014	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169015	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11169016	0.83[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11169017	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11169027	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169043	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169045	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11169048	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11169049	0.82[AMR][1000 genomes]
rs11169058	0.94[ASW][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs11169059	0.94[ASW][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs11169063	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap]
rs11169080	1.00[CHB][hapmap]
rs11611743	0.87[EUR][1000 genomes]
rs11615710	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12296440	0.88[ASW][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs12299282	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12301632	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12306118	0.83[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12306212	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12306645	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12315996	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12320284	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2272478	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3887727	1.00[CHB][hapmap]
rs4898506	0.85[YRI][hapmap]
rs57601151	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6580707	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6580709	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs6580711	0.84[EUR][1000 genomes]
rs6580715	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7132684	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7133398	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7139061	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7294648	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7295556	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7310682	1.00[JPT][hapmap]
rs73297209	0.87[EUR][1000 genomes]
rs7488923	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955541	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7962951	0.83[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7965658	0.87[GIH][hapmap]
rs7969010	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs7969099	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs7970059	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974420	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];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975712	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs7980731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11169005	HSS00289233	cis	multi-tissue	Pritchard

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49764200-49840200	Weak transcription	Fetal Lung	lung
2	chr12:49764400-49822200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:49766600-49822200	Weak transcription	NH-A	brain
4	chr12:49768400-49819200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:49783600-49816400	Weak transcription	Left Ventricle	heart
6	chr12:49788000-49822600	Weak transcription	HUVEC	blood vessel
7	chr12:49791400-49819200	Weak transcription	Osteobl	bone
8	chr12:49791800-49817000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:49792800-49812600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:49792800-49819200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:49792800-49822000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:49793000-49818600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:49794400-49812400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:49798000-49812800	Weak transcription	Fetal Intestine Small	intestine
15	chr12:49798000-49820800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:49798400-49856000	Weak transcription	Primary T cells from cord blood	blood
17	chr12:49798600-49811600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:49798600-49812400	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:49798600-49818400	Weak transcription	Fetal Stomach	stomach
20	chr12:49798600-49821800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:49798600-49822600	Weak transcription	Fetal Thymus	thymus
22	chr12:49798600-49840000	Weak transcription	Hela-S3	cervix
23	chr12:49799400-49819000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:49803000-49812400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:49807200-49817600	Enhancers	HepG2	liver
26	chr12:49807400-49818800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:49807800-49812800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:49807800-49812800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:49807800-49819600	Weak transcription	HMEC	breast
30	chr12:49807800-49822200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:49807800-49822600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:49807800-49822600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:49808000-49812400	Weak transcription	GM12878-XiMat	blood
34	chr12:49808000-49812800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:49808000-49812800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:49808200-49822400	Weak transcription	NHEK	skin
37	chr12:49808600-49814600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:49809200-49816400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:49809600-49813000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:49809800-49818400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:49810200-49814600	Weak transcription	Small Intestine	intestine
42	chr12:49810200-49814600	Weak transcription	K562	blood
43	chr12:49810200-49819800	Weak transcription	Dnd41	blood
44	chr12:49810400-49813600	Enhancers	A549	lung
45	chr12:49810600-49811600	Enhancers	Fetal Intestine Large	intestine
46	chr12:49810800-49831400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:49811000-49812600	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links