Variant report

Variant	rs2025489
Chromosome Location	chr6:87814959-87814960
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	chr6:87814512..87817505-chr6:87862895..87865178,2	K562	blood:

Variant related genes	Relation type
ENSG00000272008	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs1075068	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1080595	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1080596	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs12664578	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13191422	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1590429	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1610331	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1813847	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1813848	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1886751	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1886752	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1925687	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1925688	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1925689	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1925695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1977300	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980790	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1980792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1998765	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2025630	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2031518	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2031519	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2031520	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2031521	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2147917	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2147918	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2147919	0.91[EUR][1000 genomes]
rs2147920	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2147921	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2182181	0.91[EUR][1000 genomes]
rs2240459	0.88[EUR][1000 genomes]
rs3734187	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3812130	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3812132	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs3846776	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3857483	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3857484	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs3857485	0.90[EUR][1000 genomes]
rs3857488	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3903920	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs3904088	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs3932521	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4099964	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4110984	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4110985	0.91[EUR][1000 genomes]
rs4267927	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4269346	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4391234	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4489129	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4533962	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4540237	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4574603	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4605853	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4706289	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4707346	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs4707347	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4707348	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4707351	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4707352	0.90[EUR][1000 genomes]
rs4707356	0.89[EUR][1000 genomes]
rs4707358	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs62439493	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6454581	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6454583	0.87[EUR][1000 genomes]
rs6454584	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6454587	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6454588	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6454590	0.87[EUR][1000 genomes]
rs6454591	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6454592	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6454593	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6454594	0.90[EUR][1000 genomes]
rs6454595	0.90[EUR][1000 genomes]
rs6454598	0.88[EUR][1000 genomes]
rs6454600	0.87[EUR][1000 genomes]
rs6904310	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6907805	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6909021	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6909200	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6912970	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6913721	0.91[EUR][1000 genomes]
rs6913932	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6914193	0.92[EUR][1000 genomes]
rs6917432	0.88[EUR][1000 genomes]
rs6917455	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6917931	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6921007	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6921619	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6925648	0.88[EUR][1000 genomes]
rs6926831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs6927748	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6929920	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6933046	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6934603	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6934717	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6940544	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7739034	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7739726	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7742478	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7742710	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7748191	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7748879	0.88[EUR][1000 genomes]
rs7751029	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7752485	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7752882	0.91[EUR][1000 genomes]
rs7755244	0.90[EUR][1000 genomes]
rs7755883	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7757199	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7757827	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs7758618	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs7760278	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7761970	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7762640	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7763365	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7763371	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7766324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7767449	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7768575	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7774080	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7774603	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7774771	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7774872	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7776407	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9294367	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9294368	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9294370	0.91[EUR][1000 genomes]
rs9294371	0.89[EUR][1000 genomes]
rs9294372	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9294373	0.85[EUR][1000 genomes]
rs9344676	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9344677	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9344690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9344691	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9344693	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9344695	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9344697	0.88[EUR][1000 genomes]
rs9351114	0.80[ASN][1000 genomes]
rs9351117	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9351124	0.88[EUR][1000 genomes]
rs9353450	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9353452	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9353453	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9353455	0.80[ASN][1000 genomes]
rs9353456	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9353462	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9353463	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9353464	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9353465	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs9353468	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9359731	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9359734	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9359735	0.86[EUR][1000 genomes]
rs9359736	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9359743	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9362398	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9362400	0.86[EUR][1000 genomes]
rs9362401	0.89[EUR][1000 genomes]
rs9362408	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9362411	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9362415	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9444479	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450620	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450634	0.90[EUR][1000 genomes]
rs9450650	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9450652	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs959038	0.85[EUR][1000 genomes]
rs994170	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2025489	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs2025489	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs2025489	C6orf164	cis	Esophagus Muscularis	GTEx
rs2025489	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2025489	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs2025489	C6orf164	cis	Thyroid	GTEx
rs2025489	Hs.485895	cis	multi-tissue	Pritchard
rs2025489	C6orf164	cis	Whole Blood	GTEx
rs2025489	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87803600-87816000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:87813800-87815400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:87814000-87815000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr6:87814200-87816600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:87814400-87815800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr6:87814600-87816200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:87814800-87815200	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links