Variant report

Variant	rs6048302
Chromosome Location	chr20:22708715-22708716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:22703590..22705719-chr20:22706971..22709788,2	K562	blood:
2	chr20:22706677..22709268-chr20:22709943..22712765,2	K562	blood:
3	chr20:22708241..22708913-chr20:22785728..22786701,2	MCF-7	breast:
4	chr20:22707811..22710678-chr20:22712820..22714415,2	K562	blood:

Variant related genes	Relation type
ENSG00000265151	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10485634	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10485635	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10485636	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11087395	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11907108	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12479587	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13036614	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13036740	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13037831	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13037887	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13037911	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13037976	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13038208	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13038520	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13039038	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13039191	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13039411	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13039474	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13040538	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13040962	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13042154	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13042246	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13044630	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13044931	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13045430	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34675647	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4371419	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4514951	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4603850	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036197	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036205	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036206	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048291	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048298	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048300	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048327	0.88[EUR][1000 genomes]
rs6048328	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6075943	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6113789	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260708	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7260791	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7262725	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7263541	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7263645	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7265587	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7270196	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7270365	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7270374	0.89[TSI][hapmap]
rs7270493	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7270606	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7272556	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs745661	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8117574	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8117625	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8117637	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8117659	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8117748	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8125753	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8126106	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs965763	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs996070	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs996071	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][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	nsv1061382	chr20:22706041-22763200	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6048302	GGTLC1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22705200-22709000	Weak transcription	Right Ventricle	heart
2	chr20:22706000-22709000	Weak transcription	NHEK	skin
3	chr20:22706200-22708800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:22706200-22708800	Weak transcription	A549	lung
5	chr20:22706200-22708800	Weak transcription	Hela-S3	cervix
6	chr20:22706200-22709000	Weak transcription	HMEC	breast
7	chr20:22707600-22710000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:22708000-22710400	Enhancers	Spleen	Spleen
9	chr20:22708200-22710000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr20:22708400-22710000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr20:22708400-22710200	Enhancers	HSMM	muscle
12	chr20:22708400-22710600	Enhancers	Stomach Mucosa	stomach
13	chr20:22708600-22709400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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