Variant report

Variant	rs2250806
Chromosome Location	chr1:84596090-84596091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84594754..84597545-chr1:84597865..84602064,4	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1021490	0.81[JPT][hapmap]
rs1021491	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1057738	0.91[JPT][hapmap]
rs10874427	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10874428	0.91[JPT][hapmap]
rs10874432	0.90[JPT][hapmap]
rs11163903	0.91[JPT][hapmap]
rs11163905	0.91[JPT][hapmap]
rs11163906	0.91[JPT][hapmap]
rs11163907	0.91[JPT][hapmap]
rs11163908	0.91[JPT][hapmap]
rs11163911	0.91[JPT][hapmap]
rs11163913	0.91[JPT][hapmap]
rs12057561	0.91[JPT][hapmap]
rs12118723	0.91[JPT][hapmap]
rs12132002	0.86[JPT][hapmap]
rs12565896	0.91[JPT][hapmap]
rs12723299	0.91[JPT][hapmap]
rs12748859	0.91[JPT][hapmap]
rs12750691	0.91[JPT][hapmap]
rs12756327	0.81[EUR][1000 genomes]
rs1402694	0.91[JPT][hapmap]
rs1472243	0.91[JPT][hapmap]
rs1521518	0.95[JPT][hapmap]
rs1565823	0.82[JPT][hapmap]
rs1603000	0.93[CEU][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1874070	0.91[JPT][hapmap]
rs2037454	0.91[JPT][hapmap]
rs2134648	0.91[JPT][hapmap]
rs2134649	0.91[JPT][hapmap]
rs2642186	0.93[CEU][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2792973	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2792975	0.93[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2792976	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907193	0.85[AMR][1000 genomes]
rs4907194	0.90[JPT][hapmap]
rs594631	0.83[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs599686	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603939	0.93[CEU][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs617568	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs638545	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs648856	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs650629	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs652489	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6576959	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6576960	0.91[JPT][hapmap]
rs6576961	0.90[JPT][hapmap]
rs6576962	0.91[JPT][hapmap]
rs6576963	0.91[JPT][hapmap]
rs6695305	0.91[JPT][hapmap]
rs6695851	0.91[JPT][hapmap]
rs6696125	0.91[JPT][hapmap]
rs6699600	0.84[JPT][hapmap]
rs6701486	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6703653	0.84[ASW][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes]
rs7515976	0.91[JPT][hapmap]
rs7520283	0.84[ASW][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes]
rs7547892	0.91[JPT][hapmap]
rs903263	0.91[JPT][hapmap]
rs970318	0.82[JPT][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2250806	MCOLN2	cis	parietal	SCAN
rs2250806	LOC339524	cis	cerebellum	SCAN

Chromatin state (count:7 , 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	chr1:84584000-84609600	Weak transcription	HSMM	muscle
3	chr1:84584000-84609800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:84588000-84618400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:84590600-84607400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:84592400-84596800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:84592400-84599200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links