Variant report

Variant	rs289678
Chromosome Location	chr1:76561532-76561533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12408886	1.00[JPT][hapmap]
rs12408918	1.00[JPT][hapmap]
rs158620	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs167050	0.88[TSI][hapmap]
rs17098119	1.00[JPT][hapmap]
rs190861	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631779	1.00[JPT][hapmap]
rs289674	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289676	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289687	1.00[JPT][hapmap]
rs289692	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289693	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289701	0.88[TSI][hapmap]
rs291059	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2992503	0.82[TSI][hapmap]
rs3011995	0.88[TSI][hapmap]
rs35802431	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs384233	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs403449	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs409245	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447383	1.00[CEU][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs491409	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs50564	1.00[ASW][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs551954	0.93[EUR][1000 genomes]
rs552890	0.83[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588073	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs61558985	0.89[EUR][1000 genomes]
rs6673424	1.00[JPT][hapmap]
rs915403	0.88[TSI][hapmap]
rs915404	0.88[TSI][hapmap]

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	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76542800-76572000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:76548000-76561800	Weak transcription	Fetal Brain Female	brain
3	chr1:76548400-76576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:76557400-76561600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:76557400-76561600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:76557400-76605800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:76557600-76588800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:76558400-76562000	Enhancers	Brain Substantia Nigra	brain
9	chr1:76559000-76562000	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:76559600-76562200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:76559600-76566800	Weak transcription	Fetal Lung	lung
12	chr1:76560000-76561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:76560000-76571000	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:76560200-76573400	Weak transcription	Brain Angular Gyrus	brain
15	chr1:76560800-76562400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:76561000-76561800	Enhancers	Fetal Heart	heart
17	chr1:76561000-76562200	Enhancers	Fetal Kidney	kidney
18	chr1:76561200-76561800	Enhancers	Brain Anterior Caudate	brain
19	chr1:76561200-76561800	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr1:76561400-76561800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:76561400-76561800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:76561400-76561800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:76561400-76562000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:76561400-76562000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:76561400-76562000	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links