Variant report

Variant	rs239844
Chromosome Location	chr6:54764660-54764661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54758702..54760512-chr6:54764567..54767361,2	MCF-7	breast:
2	chr6:54761027..54762719-chr6:54763197..54766123,2	MCF-7	breast:
3	chr6:54763489..54765995-chr6:54799336..54801622,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1028423	0.80[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056630	0.92[ASN][1000 genomes]
rs1503150	0.80[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs171226	0.80[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738459	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs183011	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2397176	1.00[ASN][1000 genomes]
rs239780	0.80[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239787	0.85[CEU][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239788	0.85[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239789	0.80[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239791	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239793	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239797	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239798	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239799	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239802	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239805	0.80[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239807	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239808	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239810	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239823	0.80[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239824	0.80[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239827	0.80[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239828	0.92[ASN][1000 genomes]
rs239829	0.80[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239830	0.80[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239831	0.80[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239833	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239834	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239835	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239836	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239838	0.80[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239839	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239840	0.80[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239841	0.80[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239842	0.80[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239848	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239849	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239851	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239852	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239853	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2746440	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35620314	0.92[ASN][1000 genomes]
rs378853	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs398483	0.80[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs406149	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57835829	0.92[ASN][1000 genomes]
rs59689523	0.84[ASN][1000 genomes]
rs6917766	0.92[ASN][1000 genomes]
rs73431470	1.00[ASN][1000 genomes]
rs7743188	0.83[ASN][1000 genomes]
rs7749972	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475077	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54758000-54769400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:54758000-54775000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:54761800-54766800	Enhancers	Fetal Lung	lung
4	chr6:54762000-54769000	Weak transcription	Stomach Mucosa	stomach
5	chr6:54762000-54775000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:54762200-54775000	Weak transcription	Fetal Intestine Small	intestine
7	chr6:54763000-54765800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:54763200-54764800	Strong transcription	NHEK	skin
9	chr6:54763200-54768200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:54763600-54768600	Weak transcription	HMEC	breast
11	chr6:54763600-54775000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:54764200-54765600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:54764200-54765600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:54764200-54766000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:54764400-54764800	Enhancers	GM12878-XiMat	blood
16	chr6:54764400-54765000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr6:54764400-54765200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:54764400-54765600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr6:54764400-54765800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr6:54764600-54765000	Enhancers	H1 Cell Line	embryonic stem cell

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