Variant report

Variant	rs12724823
Chromosome Location	chr1:85906385-85906386
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10158674	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10782550	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161597	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161599	0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161614	0.85[GIH][hapmap]
rs11161615	0.81[MEX][hapmap]
rs11161616	0.85[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs11161617	0.85[CEU][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs11161618	0.84[CHB][hapmap]
rs11801146	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12049529	0.91[EUR][1000 genomes]
rs12118950	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12120551	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12122816	0.90[ASN][1000 genomes]
rs12123745	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12125900	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128907	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12129502	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12130145	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12130591	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132677	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12133722	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12135333	0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12138621	0.90[ASN][1000 genomes]
rs12138852	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12139958	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12140170	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12140272	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140457	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12140935	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12717763	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12736004	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12743049	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12758237	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12758768	0.90[ASN][1000 genomes]
rs1498374	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1608536	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17384381	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17388521	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076699	0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300639	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300640	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28529751	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34561661	0.90[ASN][1000 genomes]
rs35193119	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35240561	0.90[ASN][1000 genomes]
rs35761966	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36110608	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3768223	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71652696	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12724823	BCL10	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85886400-85914200	Weak transcription	HSMMtube	muscle
2	chr1:85893800-85916800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:85899200-85914800	Weak transcription	Esophagus	oesophagus
4	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:85902600-85912200	Weak transcription	Pancreas	Pancrea
6	chr1:85903000-85906800	Weak transcription	Lung	lung
7	chr1:85903400-85907000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:85903600-85906600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:85903600-85906800	Enhancers	Adipose Nuclei	Adipose
10	chr1:85903600-85907000	Enhancers	HepG2	liver
11	chr1:85903600-85907200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:85903600-85907200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:85903600-85907600	Enhancers	NHDF-Ad	bronchial
14	chr1:85903800-85906800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:85903800-85906800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:85903800-85907200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:85903800-85907400	Enhancers	HUVEC	blood vessel
18	chr1:85903800-85907400	Enhancers	NHLF	lung
19	chr1:85903800-85907400	Enhancers	Osteobl	bone
20	chr1:85904200-85906800	Enhancers	NH-A	brain
21	chr1:85904400-85906600	Weak transcription	Psoas Muscle	Psoas
22	chr1:85904400-85906600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:85904400-85907000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:85904400-85914800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:85904600-85910200	Weak transcription	Fetal Intestine Large	intestine
26	chr1:85904800-85906600	Enhancers	HSMM	muscle
27	chr1:85904800-85907200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr1:85905000-85906400	Weak transcription	Liver	Liver
29	chr1:85905000-85910200	Weak transcription	Fetal Intestine Small	intestine
30	chr1:85905000-85912400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:85905200-85906400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:85905200-85906600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:85905200-85912000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:85905200-85912600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:85905200-85912800	Weak transcription	Left Ventricle	heart
36	chr1:85905200-85913000	Weak transcription	Fetal Kidney	kidney
37	chr1:85905200-85914800	Weak transcription	Small Intestine	intestine
38	chr1:85905400-85907600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:85905400-85913400	Weak transcription	Fetal Lung	lung
40	chr1:85905600-85906600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:85906000-85907000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:85906000-85907000	Enhancers	Aorta	Aorta
43	chr1:85906000-85907000	Enhancers	Fetal Muscle Leg	muscle
44	chr1:85906000-85907000	Enhancers	Fetal Stomach	stomach
45	chr1:85906200-85906600	Weak transcription	Ovary	ovary
46	chr1:85906200-85906800	Enhancers	Colon Smooth Muscle	Colon
47	chr1:85906200-85907000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:85906200-85907000	Enhancers	Fetal Heart	heart
49	chr1:85906200-85907000	Enhancers	Rectal Smooth Muscle	rectum
50	chr1:85906200-85907200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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