Variant report

Variant	rs1148179
Chromosome Location	chr10:28615608-28615609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11006935	0.82[CHB][hapmap]
rs11006941	0.82[CHB][hapmap]
rs11006942	0.82[CHB][hapmap]
rs1148177	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148178	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148180	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148181	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[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];0.96[ASN][1000 genomes]
rs1148183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1148185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148187	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1148189	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12098315	1.00[ASN][1000 genomes]
rs12098711	0.82[ASN][1000 genomes]
rs12098714	0.86[ASN][1000 genomes]
rs12098807	1.00[ASN][1000 genomes]
rs12254745	0.82[CHB][hapmap]
rs1249340	0.89[ASN][1000 genomes]
rs1249347	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249348	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1273097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379320	0.82[ASN][1000 genomes]
rs16928633	0.82[CHB][hapmap]
rs1762188	0.90[ASN][1000 genomes]
rs2100614	1.00[CHB][hapmap]
rs2447629	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2995539	0.82[ASN][1000 genomes]
rs34827546	1.00[ASN][1000 genomes]
rs61845947	0.90[ASN][1000 genomes]
rs7078271	0.82[CHB][hapmap]
rs7100335	0.82[CHB][hapmap]
rs72803699	0.96[ASN][1000 genomes]
rs72805609	0.96[ASN][1000 genomes]
rs72805627	1.00[ASN][1000 genomes]
rs72805630	0.93[ASN][1000 genomes]
rs72805631	0.89[ASN][1000 genomes]
rs7898888	1.00[JPT][hapmap]
rs7911615	0.82[CHB][hapmap]
rs7916525	0.82[CHB][hapmap]
rs811496	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs813081	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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	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
3	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
4	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
5	nsv1044938	chr10:28601993-28659440	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1148179	ARHGAP12	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28596800-28618800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr10:28609200-28615800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:28614000-28619000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr10:28614400-28615800	Enhancers	Fetal Muscle Leg	muscle
5	chr10:28614600-28617800	Enhancers	Fetal Stomach	stomach
6	chr10:28614800-28617000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr10:28614800-28620600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:28615000-28616200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:28615000-28617000	Enhancers	Primary hematopoietic stem cells	blood
10	chr10:28615000-28617000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr10:28615000-28620000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr10:28615200-28615800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:28615200-28615800	Bivalent Enhancer	Fetal Brain Male	brain
14	chr10:28615200-28615800	Flanking Active TSS	Fetal Heart	heart
15	chr10:28615200-28616000	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr10:28615200-28616000	Enhancers	Fetal Lung	lung
17	chr10:28615200-28616000	Enhancers	Left Ventricle	heart
18	chr10:28615200-28616000	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr10:28615200-28616200	Enhancers	Fetal Thymus	thymus
20	chr10:28615200-28616200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr10:28615200-28616800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr10:28615200-28616800	Enhancers	Primary B cells from cord blood	blood
23	chr10:28615200-28616800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr10:28615200-28616800	Enhancers	Esophagus	oesophagus
25	chr10:28615200-28617000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr10:28615200-28617000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr10:28615200-28617000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:28615200-28617000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr10:28615200-28617000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr10:28615200-28617200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr10:28615200-28617400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:28615200-28619200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr10:28615200-28621000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:28615400-28615800	Enhancers	Small Intestine	intestine
35	chr10:28615400-28615800	Enhancers	Osteobl	bone
36	chr10:28615400-28616000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr10:28615400-28616000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:28615400-28616000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr10:28615400-28616000	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr10:28615400-28616000	Enhancers	Gastric	stomach
41	chr10:28615400-28616000	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr10:28615400-28616000	Enhancers	Hela-S3	cervix
43	chr10:28615400-28616000	Enhancers	HepG2	liver
44	chr10:28615400-28616000	Enhancers	NHEK	skin
45	chr10:28615400-28616200	Enhancers	Primary B cells from peripheral blood	blood
46	chr10:28615400-28616200	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr10:28615400-28616200	Enhancers	Ovary	ovary
48	chr10:28615400-28616800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:28615400-28617000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr10:28615400-28617000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links