Variant report

Variant	rs3899741
Chromosome Location	chr8:39953023-39953024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10282846	0.92[EUR][1000 genomes]
rs10504015	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10504016	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10504017	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12114041	0.95[EUR][1000 genomes]
rs16888751	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16888756	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888759	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888761	1.00[ASN][1000 genomes]
rs16888764	1.00[ASN][1000 genomes]
rs16888767	0.95[EUR][1000 genomes]
rs16888769	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888772	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888778	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888781	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888784	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16888789	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888796	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888801	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888804	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888805	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888807	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888813	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013398	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28567739	0.92[EUR][1000 genomes]
rs55644348	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55666363	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55704370	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55809387	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55952840	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56114060	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132784	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56180191	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56185250	0.95[EUR][1000 genomes]
rs57027362	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57281613	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57326886	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57611903	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57653585	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59995728	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60223559	0.92[EUR][1000 genomes]
rs60843978	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61566582	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6990154	0.92[EUR][1000 genomes]
rs6990874	0.92[EUR][1000 genomes]
rs72632077	0.92[EUR][1000 genomes]
rs72632084	0.92[EUR][1000 genomes]
rs72632085	0.92[EUR][1000 genomes]
rs72632088	0.92[EUR][1000 genomes]
rs72632098	0.92[EUR][1000 genomes]
rs72633009	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72633010	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs72633011	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72633012	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72633013	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633014	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633015	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633016	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633021	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633023	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633024	0.95[EUR][1000 genomes]
rs72633026	0.95[EUR][1000 genomes]
rs72633034	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633036	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633037	0.95[EUR][1000 genomes]
rs72633038	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633040	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633041	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633043	0.95[EUR][1000 genomes]
rs72633044	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633048	0.95[EUR][1000 genomes]
rs72633054	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7813461	0.92[EUR][1000 genomes]
rs7822254	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7840924	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976813	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9785157	0.95[EUR][1000 genomes]
rs9785159	0.95[EUR][1000 genomes]
rs9785174	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981193	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv539555	chr8:39683857-40673606	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv534582	chr8:39884590-40653224	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1034355	chr8:39942179-39961432	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39949200-39954800	Weak transcription	Stomach Mucosa	stomach
2	chr8:39950200-39955600	Weak transcription	Colon Smooth Muscle	Colon
3	chr8:39951000-39955400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr8:39951000-39955600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr8:39951000-39958600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr8:39951000-39968000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:39951200-39955400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr8:39951200-39955600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr8:39952000-39955200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr8:39952200-39955600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr8:39952400-39955200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr8:39952600-39955200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr8:39952600-39955200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr8:39952600-39955600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr8:39952600-39956400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr8:39952600-39957000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr8:39952600-39957000	Weak transcription	Placenta	Placenta
18	chr8:39952800-39953200	Weak transcription	A549	lung

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