Variant report

Variant	rs16963464
Chromosome Location	chr15:50526030-50526031
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50524113..50527183-chr15:50529127..50532910,3	MCF-7	breast:
2	chr15:50515572..50518632-chr15:50523853..50526982,3	K562	blood:
3	chr15:50525596..50527399-chr15:50528974..50531959,3	MCF-7	breast:
4	chr15:50473267..50475035-chr15:50524023..50526455,2	MCF-7	breast:
5	chr15:50524434..50527372-chr15:50646602..50648649,2	MCF-7	breast:
6	chr15:50523604..50526442-chr15:50529492..50532329,2	K562	blood:

Variant related genes	Relation type
ENSG00000104043	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000140284	Chromatin interaction
ENSG00000244879	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10519263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1365508	0.83[ASN][1000 genomes]
rs16963416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963436	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16963439	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16963441	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17848313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1802536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28392818	0.82[AFR][1000 genomes]
rs28420348	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28430324	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448432	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28465011	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569877	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28631084	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665566	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28715470	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28728273	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828351	0.93[ASN][1000 genomes]
rs56185295	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56306192	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493419	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493420	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493421	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162254	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175274	1.00[CEU][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7182866	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737059	0.85[AMR][1000 genomes]
rs72737086	0.81[ASN][1000 genomes]
rs8024292	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8029462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8035068	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8035897	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036826	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040691	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040819	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041910	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8043431	0.93[CEU][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9672196	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920490	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920511	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920559	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 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	chr15:50503600-50539800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr15:50508000-50539800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:50512800-50530000	Weak transcription	Colonic Mucosa	Colon
4	chr15:50514000-50531600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:50514400-50530200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:50515800-50537200	Weak transcription	Gastric	stomach
7	chr15:50518600-50530200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:50520200-50527000	Weak transcription	A549	lung
9	chr15:50520200-50537200	Weak transcription	Pancreas	Pancrea
10	chr15:50521200-50527000	Weak transcription	K562	blood
11	chr15:50521200-50531400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:50523000-50531400	Weak transcription	Fetal Intestine Large	intestine
13	chr15:50523400-50526200	Weak transcription	Fetal Intestine Small	intestine
14	chr15:50524800-50527600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr15:50525200-50529400	Genic enhancers	Liver	Liver
16	chr15:50525400-50526800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr15:50525400-50528400	Genic enhancers	Hela-S3	cervix
18	chr15:50525600-50530200	Weak transcription	HepG2	liver
19	chr15:50525800-50538600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:50526000-50527600	Strong transcription	Primary hematopoietic stem cells	blood

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