Variant report

Variant	rs16963180
Chromosome Location	chr15:50297052-50297053
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49911881..49914598-chr15:50296077..50298742,3	MCF-7	breast:
2	chr15:50295757..50297489-chr15:50308752..50310287,2	MCF-7	breast:
3	chr15:50293833..50297239-chr15:50342287..50344568,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104047	Chromatin interaction
ENSG00000166262	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11639118	1.00[CHB][hapmap]
rs12591825	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12905605	1.00[CHB][hapmap]
rs16953000	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16963141	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16963231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414001	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28630064	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356419	0.89[CEU][hapmap]
rs7168544	1.00[CHB][hapmap]
rs7177104	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7182041	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8025172	0.90[CEU][hapmap]
rs8028405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv904207	chr15:50290295-50352945	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50278000-50301600	Weak transcription	Liver	Liver
2	chr15:50293600-50297200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:50295800-50297400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:50296000-50297200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr15:50296000-50299600	Weak transcription	Fetal Heart	heart
6	chr15:50296000-50302000	Weak transcription	Fetal Intestine Small	intestine
7	chr15:50296200-50298000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:50296200-50303600	Weak transcription	Spleen	Spleen
9	chr15:50296200-50314200	Strong transcription	Primary hematopoietic stem cells	blood
10	chr15:50296400-50298800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:50296400-50301600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:50296400-50309200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr15:50296400-50311200	Weak transcription	Placenta	Placenta
14	chr15:50296400-50314600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr15:50296600-50297200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr15:50296600-50297600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:50296600-50302200	Weak transcription	Hela-S3	cervix
18	chr15:50296600-50304200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:50296800-50297600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:50296800-50335200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:50297000-50297400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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