Variant report

Variant	rs12138852
Chromosome Location	chr1:85878208-85878209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85875979..85878822-chr1:85889098..85890895,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10158674	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10782550	0.92[ASN][1000 genomes]
rs11161597	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161599	0.95[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161614	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs11161617	0.86[JPT][hapmap]
rs11161618	0.84[CHB][hapmap]
rs11801146	0.89[ASN][1000 genomes]
rs12118950	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120551	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12122816	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12123745	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125900	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128907	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12130145	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130380	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12130591	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12131926	0.89[EUR][1000 genomes]
rs12132677	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135333	0.90[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12138621	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12139958	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140170	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140272	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12140457	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140935	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12717763	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12724823	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]
rs12736004	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12743049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12758237	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758768	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498374	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1608536	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384381	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17388521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076699	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300639	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300640	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28529751	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34561661	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35193119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35240561	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35761966	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs36110608	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768223	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71652696	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85871400-85878400	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:85873200-85879600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:85873400-85882800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:85873600-85885000	Weak transcription	Fetal Intestine Large	intestine
5	chr1:85873800-85882000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:85873800-85885400	Weak transcription	Fetal Stomach	stomach
7	chr1:85873800-85887600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:85874000-85903800	Weak transcription	NHLF	lung
9	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:85874400-85903600	Weak transcription	HepG2	liver
11	chr1:85874400-85904200	Weak transcription	NH-A	brain
12	chr1:85875000-85882800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:85875400-85878800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:85875400-85880000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:85875400-85885600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:85876800-85878400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:85876800-85878400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr1:85876800-85878400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr1:85876800-85878400	Genic enhancers	Osteobl	bone
20	chr1:85876800-85880000	Strong transcription	HSMM	muscle
21	chr1:85877000-85878400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:85877000-85878800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:85877000-85879000	Enhancers	Ovary	ovary
24	chr1:85877000-85880400	Enhancers	NHDF-Ad	bronchial
25	chr1:85877200-85878800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:85877200-85885600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:85877400-85879400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:85877400-85882400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:85877600-85878600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:85877600-85879200	Weak transcription	HUVEC	blood vessel
31	chr1:85877600-85882400	Weak transcription	Psoas Muscle	Psoas
32	chr1:85877600-85882800	Weak transcription	Aorta	Aorta
33	chr1:85877600-85882800	Weak transcription	Pancreas	Pancrea
34	chr1:85877600-85882800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:85877600-85885800	Weak transcription	HSMMtube	muscle
36	chr1:85877800-85882600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:85878000-85883800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:85878200-85880600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:85878200-85882600	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links