Variant report

Variant	rs2742496
Chromosome Location	chr11:8965350-8965351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10219366	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1025438	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10734639	0.91[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs10769974	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs10769976	0.98[EUR][1000 genomes]
rs10769977	0.91[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840150	0.87[EUR][1000 genomes]
rs10840151	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs10840153	0.81[EUR][1000 genomes]
rs10840154	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs10840155	0.82[EUR][1000 genomes]
rs10840156	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042121	0.85[EUR][1000 genomes]
rs11042128	0.80[EUR][1000 genomes]
rs11042131	0.82[EUR][1000 genomes]
rs1133833	0.81[MEX][hapmap]
rs1136966	0.86[MEX][hapmap]
rs12785559	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12786377	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12790020	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12794962	0.84[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12798311	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12805109	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1347016	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1985026	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2016844	0.92[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2043218	0.81[EUR][1000 genomes]
rs2056903	0.91[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060157	0.81[AMR][1000 genomes]
rs2116510	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2116511	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163625	0.91[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2246878	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247038	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2252102	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2316523	0.80[EUR][1000 genomes]
rs2316541	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568029	0.80[MEX][hapmap]
rs2568034	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2568042	1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs2568047	0.84[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2568069	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568074	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568075	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568077	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568079	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568081	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568086	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568087	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568088	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2653556	0.96[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs2653562	0.81[EUR][1000 genomes]
rs2653565	1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2653587	0.85[EUR][1000 genomes]
rs2653590	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653594	0.81[ASN][1000 genomes]
rs2653597	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2653601	0.92[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2653604	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742473	0.85[ASN][1000 genomes]
rs2742486	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742487	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742488	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742489	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2742491	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742493	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742497	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742502	0.86[MEX][hapmap]
rs2742504	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742512	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742513	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742514	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[ASN][1000 genomes]
rs2742519	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs2742521	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3751063	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs3751066	0.91[CEU][hapmap]
rs3751068	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs3763911	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs3763912	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4370967	0.84[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4909951	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs4910181	0.93[EUR][1000 genomes]
rs4910313	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7106152	0.82[EUR][1000 genomes]
rs7124403	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7125458	0.81[MEX][hapmap]
rs72851596	0.90[ASN][1000 genomes]
rs72852790	0.95[ASN][1000 genomes]
rs72853712	0.95[ASN][1000 genomes]
rs7932377	0.82[EUR][1000 genomes]
rs7936201	0.81[MEX][hapmap]
rs7940895	0.88[ASN][1000 genomes]
rs7942026	0.83[ASN][1000 genomes]
rs7951226	0.82[EUR][1000 genomes]
rs909464	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9300096	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs982273	0.95[CEU][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2742496	C11orf17	cis	multi-tissue	Pritchard
rs2742496	OR52E6	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8943800-8969200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:8944600-8985000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:8945800-8974000	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:8947000-8968800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:8947000-8977000	Weak transcription	Aorta	Aorta
6	chr11:8947400-8969000	Weak transcription	Thymus	Thymus
7	chr11:8947600-8969000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:8948200-8969000	Weak transcription	Fetal Brain Female	brain
9	chr11:8948600-8969200	Weak transcription	Gastric	stomach
10	chr11:8948600-8969200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:8951200-8974400	Weak transcription	HepG2	liver
12	chr11:8952600-8975800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:8952800-8968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:8954400-8984400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:8955200-8976200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:8955800-8968000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:8956800-8968600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:8956800-8969000	Weak transcription	Osteobl	bone
19	chr11:8957000-8968000	Weak transcription	HSMM	muscle
20	chr11:8957000-8968800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:8957000-8968800	Weak transcription	Fetal Intestine Large	intestine
22	chr11:8957000-8969000	Weak transcription	HSMMtube	muscle
23	chr11:8957000-8969800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr11:8957000-8969800	Weak transcription	Fetal Stomach	stomach
25	chr11:8957000-8974200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:8957000-8980800	Weak transcription	Fetal Heart	heart
27	chr11:8957200-8968800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:8957200-8968800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:8957200-8969000	Weak transcription	A549	lung
30	chr11:8957200-8969200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr11:8957200-8970200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:8957200-8973400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:8957400-8968600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:8957400-8968800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:8957400-8969000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:8957400-8969000	Weak transcription	Fetal Thymus	thymus
37	chr11:8957400-8969000	Weak transcription	NH-A	brain
38	chr11:8957400-8969800	Weak transcription	Spleen	Spleen
39	chr11:8958800-8969000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:8959000-8968800	Weak transcription	Placenta	Placenta
41	chr11:8959000-8974000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:8959200-8970600	Weak transcription	Fetal Kidney	kidney
43	chr11:8960800-8969200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:8962400-8968600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:8962800-8971800	Weak transcription	NHDF-Ad	bronchial
46	chr11:8963000-8969000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:8963200-8967800	Weak transcription	Pancreas	Pancrea
48	chr11:8963200-8968800	Weak transcription	Left Ventricle	heart
49	chr11:8963200-8968800	Weak transcription	Ovary	ovary
50	chr11:8963200-8969000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links