Variant report

Variant	rs16963441
Chromosome Location	chr15:50519673-50519674
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50510973..50514967-chr15:50518126..50521413,6	MCF-7	breast:
2	chr15:50473348..50474244-chr15:50519432..50519938,2	MCF-7	breast:
3	chr15:50517837..50520977-chr15:50646044..50647800,3	MCF-7	breast:
4	chr15:50519543..50521408-chr15:50526964..50529352,2	K562	blood:

Variant related genes	Relation type
ENSG00000104064	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000200605	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10519263	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329426	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329489	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13329494	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1365508	0.83[ASN][1000 genomes]
rs16963416	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963420	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963426	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16963436	0.83[AMR][1000 genomes]
rs16963439	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs16963451	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963464	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415862	0.82[MEX][hapmap];0.86[AMR][1000 genomes]
rs17848313	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1802536	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs2414037	0.80[AMR][1000 genomes]
rs2414040	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28420348	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28430324	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28448432	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28465011	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505254	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569877	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28631084	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665566	0.93[ASN][1000 genomes]
rs28715470	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28715698	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28728273	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34490804	0.80[AMR][1000 genomes]
rs3803371	0.92[CEU][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes]
rs55740521	0.86[AMR][1000 genomes]
rs55828351	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55852503	0.83[AMR][1000 genomes]
rs56083537	0.86[AMR][1000 genomes]
rs56185295	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56306192	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493419	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493420	0.85[AMR][1000 genomes]
rs6493421	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493422	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66472276	0.90[AMR][1000 genomes]
rs7162254	1.00[ASN][1000 genomes]
rs7162842	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs7163191	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7175274	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7182866	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737046	0.80[AMR][1000 genomes]
rs72737047	0.83[AMR][1000 genomes]
rs72737057	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72737059	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72737086	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73395114	0.90[AMR][1000 genomes]
rs8024292	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs8029462	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8030902	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8035068	1.00[ASN][1000 genomes]
rs8035897	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8036826	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8039502	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040691	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040819	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041232	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041589	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041910	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8043431	0.86[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9672196	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920490	0.85[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs9920511	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs9920559	0.85[CEU][hapmap];0.83[AMR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16963441	SLC24A5	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50503600-50519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:50503600-50539800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:50508000-50539800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:50511800-50525400	Strong transcription	Hela-S3	cervix
5	chr15:50512800-50530000	Weak transcription	Colonic Mucosa	Colon
6	chr15:50513800-50525200	Weak transcription	Stomach Mucosa	stomach
7	chr15:50513800-50525400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:50514000-50524600	Weak transcription	Primary B cells from cord blood	blood
9	chr15:50514000-50531600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:50514400-50530200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:50514600-50519800	Weak transcription	Esophagus	oesophagus
12	chr15:50515800-50537200	Weak transcription	Gastric	stomach
13	chr15:50518000-50524800	Weak transcription	Fetal Kidney	kidney
14	chr15:50518600-50530200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:50519000-50519800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:50519000-50520200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:50519200-50519800	Genic enhancers	Liver	Liver
18	chr15:50519200-50520200	Enhancers	NHLF	lung
19	chr15:50519200-50521400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr15:50519200-50524000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:50519200-50525800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:50519400-50519800	Enhancers	NH-A	brain
23	chr15:50519400-50519800	Enhancers	NHDF-Ad	bronchial
24	chr15:50519400-50520200	Genic enhancers	Fetal Intestine Large	intestine
25	chr15:50519400-50520200	Strong transcription	Pancreas	Pancrea
26	chr15:50519400-50520400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr15:50519400-50521200	Strong transcription	K562	blood
28	chr15:50519400-50521800	Strong transcription	HepG2	liver
29	chr15:50519400-50523400	Strong transcription	Fetal Intestine Small	intestine
30	chr15:50519600-50520200	Genic enhancers	A549	lung
31	chr15:50519600-50521200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:50519600-50521200	Weak transcription	Osteobl	bone

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