Variant report

Variant	rs7088552
Chromosome Location	chr10:28490529-28490530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10508736	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10740785	0.95[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs10740786	0.97[ASN][1000 genomes]
rs10763646	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10763647	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10763648	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10763649	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10763650	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10826406	0.82[JPT][hapmap]
rs10826414	0.97[ASN][1000 genomes]
rs10826415	0.96[ASN][1000 genomes]
rs10826417	0.97[ASN][1000 genomes]
rs10826418	0.97[ASN][1000 genomes]
rs10826419	0.97[ASN][1000 genomes]
rs10826420	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10826421	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826422	0.97[ASN][1000 genomes]
rs10826424	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10826425	0.90[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs11006894	0.82[JPT][hapmap]
rs11006896	0.82[CHB][hapmap]
rs11006897	0.82[CHB][hapmap]
rs11006902	0.82[CHB][hapmap]
rs11006903	0.81[CHB][hapmap]
rs11006914	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11006915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006917	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11006957	0.81[JPT][hapmap]
rs12049636	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12221232	0.97[ASN][1000 genomes]
rs12248472	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12251587	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][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]
rs12251924	0.82[CHB][hapmap]
rs12254584	0.82[CHB][hapmap]
rs12255686	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261363	0.85[CHB][hapmap]
rs12264184	0.82[CHB][hapmap]
rs12268470	0.82[CHB][hapmap]
rs12357915	0.96[ASN][1000 genomes]
rs12766231	0.82[CHB][hapmap]
rs1418759	0.83[CHD][hapmap]
rs17831690	0.96[ASN][1000 genomes]
rs1824172	0.97[ASN][1000 genomes]
rs1824173	0.96[ASN][1000 genomes]
rs1870097	0.82[JPT][hapmap]
rs1937807	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1937808	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1937809	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2607539	0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2607542	0.97[ASN][1000 genomes]
rs2607543	0.97[ASN][1000 genomes]
rs2607544	0.97[ASN][1000 genomes]
rs2607545	0.97[ASN][1000 genomes]
rs2607546	0.97[ASN][1000 genomes]
rs2801833	0.97[ASN][1000 genomes]
rs2801834	0.91[ASN][1000 genomes]
rs2801835	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2985521	0.97[ASN][1000 genomes]
rs2985535	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2997210	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35494924	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3847382	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3901407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4018718	0.97[ASN][1000 genomes]
rs4568902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][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]
rs4749310	0.80[JPT][hapmap]
rs6481515	0.83[CHD][hapmap]
rs7067826	0.97[ASN][1000 genomes]
rs7068246	0.93[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7068687	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7081378	0.82[CHB][hapmap]
rs7085245	0.82[CHB][hapmap]
rs7096944	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7101051	0.82[CHB][hapmap]
rs72631847	0.97[ASN][1000 genomes]
rs7893311	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7901941	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7913970	0.83[CHD][hapmap]
rs7915273	0.97[ASN][1000 genomes]
rs7922685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831816	chr10:28304698-28493635	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv831817	chr10:28369836-28539930	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv6188	chr10:28489076-28514068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7088552	MKX	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28449800-28497000	Weak transcription	Fetal Intestine Small	intestine
2	chr10:28467600-28491800	Weak transcription	Psoas Muscle	Psoas
3	chr10:28467600-28525600	Weak transcription	Aorta	Aorta
4	chr10:28467800-28495200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:28469800-28491000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr10:28481000-28496400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr10:28484600-28492400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr10:28484600-28496800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:28485000-28490800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:28485600-28504400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr10:28486800-28496200	Weak transcription	Primary B cells from cord blood	blood
12	chr10:28487600-28491200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr10:28487600-28497800	Weak transcription	HepG2	liver
14	chr10:28487600-28529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:28487800-28491400	Strong transcription	Primary T cells from cord blood	blood
16	chr10:28487800-28492200	Enhancers	HSMMtube	muscle
17	chr10:28488000-28490800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:28488600-28491600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr10:28488600-28491800	Enhancers	Hela-S3	cervix
20	chr10:28488600-28492200	Enhancers	HSMM	muscle
21	chr10:28488600-28500200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr10:28489000-28490800	Enhancers	Colon Smooth Muscle	Colon
23	chr10:28489000-28492200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr10:28489000-28492600	Enhancers	Rectal Smooth Muscle	rectum
25	chr10:28489200-28491800	Weak transcription	Fetal Muscle Leg	muscle
26	chr10:28489200-28496800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr10:28489600-28492200	Enhancers	Fetal Lung	lung
28	chr10:28489600-28493400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:28489800-28504400	Weak transcription	Esophagus	oesophagus
30	chr10:28490000-28490600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:28490000-28491000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr10:28490200-28490600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr10:28490200-28491800	Bivalent Enhancer	Osteobl	bone
34	chr10:28490200-28492200	Enhancers	Fetal Stomach	stomach
35	chr10:28490400-28490600	Enhancers	Small Intestine	intestine
36	chr10:28490400-28490600	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr10:28490400-28490800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:28490400-28490800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr10:28490400-28491200	Strong transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links