Variant report

Variant	rs2139931
Chromosome Location	chr1:84590527-84590528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1016379	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031206	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036564	0.85[CEU][hapmap]
rs2221360	0.81[EUR][1000 genomes]
rs2642181	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642182	1.00[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642183	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2642184	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[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];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2684911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684914	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684916	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2811998	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2811999	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812001	0.92[EUR][1000 genomes]
rs2812447	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2812451	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812452	1.00[CEU][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs2812453	0.96[EUR][1000 genomes]
rs512737	0.81[CHB][hapmap];0.82[YRI][hapmap]
rs59627911	0.80[AFR][1000 genomes]
rs626376	0.82[CHD][hapmap]
rs663521	0.82[ASN][1000 genomes]
rs667304	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs680905	0.82[CHD][hapmap]
rs72710880	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72710887	0.81[EUR][1000 genomes]
rs72711180	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74095506	0.80[AFR][1000 genomes]
rs7530801	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs810915	0.82[CHD][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	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv546690	chr1:84562265-84655238	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84569200-84599600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:84576000-84591800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:84584000-84591000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:84584000-84592600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:84584000-84609600	Weak transcription	HSMM	muscle
6	chr1:84584000-84609800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:84587600-84591400	Weak transcription	Fetal Stomach	stomach
8	chr1:84587800-84594400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:84588000-84591800	Weak transcription	Ovary	ovary
10	chr1:84588000-84618400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:84588200-84593600	Weak transcription	Brain Substantia Nigra	brain
12	chr1:84589600-84591800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:84589800-84591400	Enhancers	Fetal Heart	heart
14	chr1:84590200-84590600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:84590200-84591200	Enhancers	Right Atrium	heart
16	chr1:84590200-84591200	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links