Variant report

Variant	rs7711576
Chromosome Location	chr5:80926660-80926661
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10514230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10942274	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10942275	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs11738820	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11743304	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11745832	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11749863	0.93[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12514473	0.80[CEU][hapmap]
rs12517941	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12521077	0.90[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs12521151	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13157978	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13158214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13170372	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13171787	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13173845	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13184174	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13436668	0.93[CEU][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1971177	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060584	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34307657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34365981	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34870295	0.88[ASN][1000 genomes]
rs35340025	0.85[EUR][1000 genomes]
rs35862056	0.97[ASN][1000 genomes]
rs4529168	0.82[CEU][hapmap]
rs62366269	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62368677	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62368679	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6874274	0.91[MEX][hapmap]
rs6887473	0.88[ASN][1000 genomes]
rs71636282	0.95[ASN][1000 genomes]
rs72773052	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7707981	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7720445	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7726379	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882233	chr5:80849084-81049187	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv882234	chr5:80853708-80966666	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv525437	chr5:80876359-80964452	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv462222	chr5:80900719-80964452	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv598752	chr5:80900719-80964452	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv882235	chr5:80909132-81006061	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv830361	chr5:80909811-81080409	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7711576	TBCA	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80906000-80927000	Weak transcription	Gastric	stomach
2	chr5:80906000-80929400	Weak transcription	Fetal Brain Female	brain
3	chr5:80906000-80935000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:80906000-80946600	Weak transcription	Brain Anterior Caudate	brain
5	chr5:80906000-80947000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:80906200-80927000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:80906200-80927200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:80906200-80927600	Weak transcription	Lung	lung
9	chr5:80906200-80930600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:80906200-80933000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:80906200-80938800	Weak transcription	Left Ventricle	heart
12	chr5:80906200-80942400	Weak transcription	Esophagus	oesophagus
13	chr5:80906200-80947800	Weak transcription	Brain Germinal Matrix	brain
14	chr5:80906600-80936200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:80909600-80933200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:80910000-80930600	Weak transcription	Adipose Nuclei	Adipose
17	chr5:80910400-80953000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:80910800-80949200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr5:80918200-80934800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:80918400-80938800	Weak transcription	Fetal Stomach	stomach
21	chr5:80918400-80939800	Weak transcription	Fetal Lung	lung
22	chr5:80918800-80935200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:80920600-80946800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr5:80921200-80927000	Weak transcription	Small Intestine	intestine
25	chr5:80921200-80983000	Weak transcription	Aorta	Aorta
26	chr5:80922600-80929400	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:80922600-80933600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:80922600-80935800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:80922600-80937600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:80922800-80934600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:80922800-80935000	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:80923000-80952800	Weak transcription	Fetal Intestine Large	intestine
33	chr5:80923200-80927400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:80923200-80929800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:80923200-80930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:80923200-80934200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:80923200-80934400	Weak transcription	NHDF-Ad	bronchial
38	chr5:80923200-80942000	Weak transcription	Fetal Intestine Small	intestine
39	chr5:80923200-80947000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:80923200-80948400	Weak transcription	K562	blood
41	chr5:80923400-80927000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:80923400-80930400	Weak transcription	Fetal Heart	heart
43	chr5:80923400-80934600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:80923400-80934600	Weak transcription	NHLF	lung
45	chr5:80923400-80934600	Weak transcription	Osteobl	bone
46	chr5:80923400-80938400	Weak transcription	HUVEC	blood vessel
47	chr5:80923600-80927800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:80923600-80933400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:80923800-80932800	Weak transcription	Psoas Muscle	Psoas
50	chr5:80923800-80936000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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