Variant report

Variant	rs7945705
Chromosome Location	chr11:8862530-8862531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10743093	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10769947	0.81[CEU][hapmap]
rs10769948	0.81[CEU][hapmap]
rs10769957	0.81[CEU][hapmap]
rs10769967	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10769968	0.81[EUR][1000 genomes]
rs10769970	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes]
rs10769971	0.85[CEU][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes]
rs10769973	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes]
rs10769979	0.93[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs10840130	0.92[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10840134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840141	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs10840142	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10840147	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs10840148	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs11042059	0.81[CEU][hapmap]
rs11042078	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs11042079	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11042082	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11042088	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11042102	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042103	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042125	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs11042149	0.81[CEU][hapmap]
rs11042151	0.86[ASW][hapmap];0.93[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs11042154	0.93[CEU][hapmap]
rs1123936	0.85[CEU][hapmap]
rs11603841	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs12224436	0.81[CEU][hapmap]
rs12794444	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1529641	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1560569	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs1569408	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1883098	0.81[EUR][1000 genomes]
rs1980428	0.85[CEU][hapmap]
rs1980429	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs1988708	0.81[EUR][1000 genomes]
rs1988709	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2016942	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs2316865	0.81[CEU][hapmap]
rs2568043	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568045	0.85[CEU][hapmap]
rs2568054	0.81[EUR][1000 genomes]
rs2568059	0.83[EUR][1000 genomes]
rs2568061	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2568062	0.82[EUR][1000 genomes]
rs2568065	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes]
rs2568090	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2653567	0.81[EUR][1000 genomes]
rs2653570	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs2653593	0.83[EUR][1000 genomes]
rs2653605	0.85[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs2653606	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2653607	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2653616	0.82[EUR][1000 genomes]
rs2742480	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs2742536	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs2742537	0.87[CEU][hapmap]
rs2742540	0.92[CEU][hapmap];0.82[MEX][hapmap]
rs2742545	0.92[CEU][hapmap]
rs2742550	0.82[EUR][1000 genomes]
rs2742552	0.92[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap]
rs34842234	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3763918	0.81[CEU][hapmap]
rs4554887	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4909952	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4910062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910119	0.80[AMR][1000 genomes]
rs4910442	0.84[CEU][hapmap]
rs4929911	0.81[CEU][hapmap]
rs4929912	0.81[CEU][hapmap]
rs4929914	0.81[CEU][hapmap]
rs4929922	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs61876187	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6486060	0.85[CEU][hapmap]
rs7119939	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123429	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7123861	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7479407	0.93[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs7925728	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs7930026	0.92[CEU][hapmap]
rs7937298	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7943377	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7947631	0.85[CEU][hapmap]
rs905290	0.80[CEU][hapmap]
rs978636	0.80[AMR][1000 genomes];0.94[EUR][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	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

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7945705	RRP8	cis	parietal	SCAN
rs7945705	ST5	cis	parietal	SCAN
rs7945705	AKIP1	cis	Thyroid	GTEx
rs7945705	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs7945705	OR51A7	cis	cerebellum	SCAN
rs7945705	TRIM22	cis	parietal	SCAN
rs7945705	WEE1	cis	parietal	SCAN
rs7945705	OR51B6	cis	parietal	SCAN
rs7945705	TMEM9B	cis	parietal	SCAN
rs7945705	MRVI1	cis	cerebellum	SCAN
rs7945705	OR52E8	cis	cerebellum	SCAN
rs7945705	TMEM9B-AS1	cis	lung	GTEx
rs7945705	C11orf17	cis	cerebellum	SCAN
rs7945705	NRIP3	cis	parietal	SCAN
rs7945705	OR52A1	cis	parietal	SCAN
rs7945705	APBB1	cis	parietal	SCAN
rs7945705	OR51Q1	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8858600-8862600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:8859200-8862600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:8859200-8862600	Enhancers	Fetal Lung	lung
4	chr11:8859200-8862600	Enhancers	Small Intestine	intestine
5	chr11:8859400-8862600	Enhancers	HMEC	breast
6	chr11:8859400-8864000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:8859600-8863000	Enhancers	Fetal Muscle Leg	muscle
8	chr11:8859800-8862600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr11:8859800-8862600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr11:8859800-8862600	Enhancers	Duodenum Mucosa	Duodenum
11	chr11:8859800-8862600	Enhancers	Fetal Kidney	kidney
12	chr11:8859800-8863200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr11:8859800-8863800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr11:8860000-8862600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr11:8860000-8862800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:8860000-8863200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:8860200-8862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:8860200-8862800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:8860200-8863400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:8860400-8862600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:8860600-8863600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr11:8860600-8864400	Weak transcription	Osteobl	bone
23	chr11:8861000-8862600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:8861000-8862600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr11:8861000-8862600	Enhancers	HUVEC	blood vessel
26	chr11:8861000-8862600	Enhancers	NH-A	brain
27	chr11:8861000-8863200	Enhancers	Fetal Muscle Trunk	muscle
28	chr11:8861200-8862600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:8861200-8862600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:8861200-8862600	Enhancers	Fetal Intestine Large	intestine
31	chr11:8861200-8863000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr11:8861400-8862600	Enhancers	Brain Anterior Caudate	brain
33	chr11:8861400-8862600	Enhancers	Brain Substantia Nigra	brain
34	chr11:8861400-8862600	Enhancers	A549	lung
35	chr11:8861400-8862600	Enhancers	NHEK	skin
36	chr11:8861600-8862600	Enhancers	Brain Cingulate Gyrus	brain
37	chr11:8861600-8863200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:8862000-8863600	Enhancers	HepG2	liver
39	chr11:8862000-8864600	Weak transcription	NHDF-Ad	bronchial
40	chr11:8862200-8863000	Enhancers	Stomach Smooth Muscle	stomach
41	chr11:8862200-8863400	Weak transcription	Fetal Intestine Small	intestine
42	chr11:8862200-8881200	Weak transcription	Hela-S3	cervix
43	chr11:8862400-8862600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr11:8862400-8862600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr11:8862400-8862600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:8862400-8862600	Enhancers	Brain Hippocampus Middle	brain
47	chr11:8862400-8863000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr11:8862400-8864800	Weak transcription	Fetal Stomach	stomach
49	chr11:8862400-8865000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:8862400-8865000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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