Variant report

Variant	rs71423929
Chromosome Location	chr2:47155984-47155985
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47151428..47156852-chr2:47167376..47169782,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10174894	0.96[ASN][1000 genomes]
rs10190862	0.88[EUR][1000 genomes]
rs10190882	0.88[EUR][1000 genomes]
rs10197474	0.88[EUR][1000 genomes]
rs10199965	0.94[ASN][1000 genomes]
rs11890177	0.94[ASN][1000 genomes]
rs11894319	0.96[ASN][1000 genomes]
rs13388612	1.00[ASN][1000 genomes]
rs13392448	0.94[ASN][1000 genomes]
rs13394007	0.88[EUR][1000 genomes]
rs13398851	0.87[ASN][1000 genomes]
rs13410702	0.88[EUR][1000 genomes]
rs13415655	0.88[EUR][1000 genomes]
rs13415771	0.88[EUR][1000 genomes]
rs13419072	0.88[EUR][1000 genomes]
rs1446499	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1446500	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17035813	0.81[EUR][1000 genomes]
rs17035823	0.81[EUR][1000 genomes]
rs17035859	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17035867	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17035884	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17035887	0.94[ASN][1000 genomes]
rs2084192	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289927	0.96[ASN][1000 genomes]
rs2289928	0.96[ASN][1000 genomes]
rs2347259	0.88[ASN][1000 genomes]
rs28516550	0.94[ASN][1000 genomes]
rs3087857	1.00[ASN][1000 genomes]
rs34581142	0.96[ASN][1000 genomes]
rs35433380	0.96[ASN][1000 genomes]
rs4505575	0.81[ASN][1000 genomes]
rs55872217	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56213467	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58589709	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60194846	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61132855	0.88[ASN][1000 genomes]
rs62136788	0.88[EUR][1000 genomes]
rs62136818	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136819	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136820	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62136822	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136823	0.96[ASN][1000 genomes]
rs62136825	0.96[ASN][1000 genomes]
rs62136827	0.96[ASN][1000 genomes]
rs62140550	1.00[ASN][1000 genomes]
rs62140553	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62140556	0.88[AMR][1000 genomes]
rs6544938	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544939	0.98[ASN][1000 genomes]
rs6706031	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6714269	0.81[EUR][1000 genomes]
rs6715391	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715620	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716381	1.00[ASN][1000 genomes]
rs6722440	0.96[ASN][1000 genomes]
rs6729120	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729604	1.00[ASN][1000 genomes]
rs6733548	1.00[ASN][1000 genomes]
rs6743966	0.94[ASN][1000 genomes]
rs6743994	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745578	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6755303	0.98[ASN][1000 genomes]
rs6758093	1.00[ASN][1000 genomes]
rs6758512	0.96[ASN][1000 genomes]
rs720827	0.88[EUR][1000 genomes]
rs7340475	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73926966	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754411	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7565420	0.90[ASN][1000 genomes]
rs7574514	0.85[ASN][1000 genomes]
rs7574833	0.83[ASN][1000 genomes]
rs7575172	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586004	0.94[ASN][1000 genomes]
rs7596198	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601491	1.00[ASN][1000 genomes]
rs8861	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9973504	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47144200-47157200	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:47144200-47166600	Weak transcription	Pancreas	Pancrea
3	chr2:47144600-47164600	Weak transcription	Spleen	Spleen
4	chr2:47144800-47167000	Weak transcription	Fetal Lung	lung
5	chr2:47146000-47167400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:47150600-47156600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:47150600-47166600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:47150600-47167000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:47150800-47157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:47151000-47166800	Weak transcription	Small Intestine	intestine
11	chr2:47153400-47164400	Weak transcription	Thymus	Thymus
12	chr2:47153600-47160200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:47153800-47166600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:47154000-47166400	Weak transcription	Hela-S3	cervix
15	chr2:47154400-47163600	Weak transcription	Osteobl	bone
16	chr2:47154400-47166800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:47154600-47159400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr2:47155200-47156400	Enhancers	Dnd41	blood
19	chr2:47155200-47164400	Weak transcription	Fetal Thymus	thymus
20	chr2:47155600-47156000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:47155600-47159800	Weak transcription	Primary B cells from cord blood	blood
22	chr2:47155800-47166600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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