Variant report

Variant	rs10889313
Chromosome Location	chr1:62707256-62707257
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62679033..62681110-chr1:62704985..62707822,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1050334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10789108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889309	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10889310	0.85[ASN][1000 genomes]
rs10889315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11207941	0.99[ASN][1000 genomes]
rs11207942	0.92[ASN][1000 genomes]
rs11207943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207944	1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs11207945	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs11207946	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207947	0.87[ASN][1000 genomes]
rs11207948	0.86[ASN][1000 genomes]
rs12030846	0.92[ASN][1000 genomes]
rs12089897	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12096118	0.84[ASN][1000 genomes]
rs12120789	0.99[ASN][1000 genomes]
rs12138777	0.95[ASN][1000 genomes]
rs12144282	0.99[ASN][1000 genomes]
rs2067994	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457812	0.87[ASN][1000 genomes]
rs2481689	0.83[ASN][1000 genomes]
rs2666478	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2774928	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs41289438	0.99[ASN][1000 genomes]
rs4322258	0.91[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs55673263	0.86[ASN][1000 genomes]
rs56318037	0.85[ASN][1000 genomes]
rs61775734	0.99[ASN][1000 genomes]
rs61775736	0.99[ASN][1000 genomes]
rs61775737	0.99[ASN][1000 genomes]
rs6660963	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664672	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6680953	0.99[ASN][1000 genomes]
rs6688986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6696307	1.00[ASN][1000 genomes]
rs6696486	0.99[ASN][1000 genomes]
rs7553446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62701000-62707400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:62701000-62710800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:62701400-62709400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:62704000-62710600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:62704000-62711400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:62704000-62720600	Weak transcription	Right Atrium	heart
7	chr1:62704200-62711600	Weak transcription	Adipose Nuclei	Adipose
8	chr1:62704200-62712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:62704400-62713200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:62706000-62708800	Enhancers	Fetal Stomach	stomach
11	chr1:62706400-62707400	Enhancers	A549	lung
12	chr1:62706400-62707800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:62706400-62707800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:62706400-62707800	Enhancers	Fetal Muscle Trunk	muscle
15	chr1:62706400-62708000	Enhancers	Fetal Muscle Leg	muscle
16	chr1:62706400-62708400	Enhancers	Placenta	Placenta
17	chr1:62706400-62713200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:62706600-62707600	Enhancers	HSMM	muscle
19	chr1:62706600-62707800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:62706600-62707800	Enhancers	Fetal Lung	lung
21	chr1:62706600-62708000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:62706600-62708000	Enhancers	Fetal Heart	heart
23	chr1:62706800-62707400	Enhancers	Brain Anterior Caudate	brain
24	chr1:62706800-62707600	Enhancers	Fetal Thymus	thymus
25	chr1:62706800-62707600	Enhancers	Right Ventricle	heart
26	chr1:62706800-62707800	Enhancers	Colon Smooth Muscle	Colon
27	chr1:62706800-62707800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr1:62706800-62707800	Enhancers	Left Ventricle	heart
29	chr1:62706800-62707800	Enhancers	Pancreas	Pancrea
30	chr1:62706800-62707800	Enhancers	HSMMtube	muscle
31	chr1:62706800-62708000	Enhancers	Liver	Liver
32	chr1:62706800-62708000	Flanking Active TSS	HepG2	liver
33	chr1:62707000-62707400	Enhancers	Stomach Mucosa	stomach
34	chr1:62707000-62707600	Enhancers	Fetal Kidney	kidney
35	chr1:62707000-62707600	Enhancers	Gastric	stomach
36	chr1:62707000-62707600	Enhancers	Lung	lung
37	chr1:62707000-62707800	Enhancers	Colonic Mucosa	Colon
38	chr1:62707000-62707800	Enhancers	Fetal Intestine Large	intestine
39	chr1:62707200-62707400	Enhancers	Hela-S3	cervix
40	chr1:62707200-62707600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:62707200-62710600	Weak transcription	HMEC	breast
42	chr1:62707200-62710800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links