Variant report

Variant	rs16962999
Chromosome Location	chr15:50159659-50159660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50155057..50157653-chr15:50158605..50160734,2	K562	blood:
2	chr15:50115862..50118936-chr15:50156885..50160931,3	MCF-7	breast:
3	chr15:49911649..49914161-chr15:50159017..50160535,2	MCF-7	breast:
4	chr15:50158299..50161913-chr15:50163926..50167616,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166262	Chromatin interaction
ENSG00000104047	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10519242	0.83[ASN][1000 genomes]
rs1059851	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1059852	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11070733	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630021	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11632077	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11632116	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11633343	0.91[CEU][hapmap]
rs11633465	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11633470	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11633571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11633714	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11633744	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11633759	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs11634914	0.80[EUR][1000 genomes]
rs12185124	0.83[ASN][1000 genomes]
rs12903153	0.80[EUR][1000 genomes]
rs12907836	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12909447	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914231	1.00[JPT][hapmap]
rs12915207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs13329598	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16962994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17486097	0.92[CEU][hapmap]
rs17486425	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17486446	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17486544	0.80[EUR][1000 genomes]
rs17487811	1.00[JPT][hapmap]
rs2413975	1.00[JPT][hapmap]
rs28550208	0.83[ASN][1000 genomes]
rs28706888	0.83[ASN][1000 genomes]
rs34404202	0.81[EUR][1000 genomes]
rs34845057	0.87[EUR][1000 genomes]
rs4275793	0.80[EUR][1000 genomes]
rs4347574	0.91[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4494482	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4494483	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4544192	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61618346	0.86[EUR][1000 genomes]
rs6493383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66809683	0.87[EUR][1000 genomes]
rs7170482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172553	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7172585	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72733056	0.80[EUR][1000 genomes]
rs7497350	1.00[JPT][hapmap]
rs8025533	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs8031452	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs8036570	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs8038434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041979	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042458	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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	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	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr15:50135200-50181400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:50135800-50187400	Weak transcription	Liver	Liver
3	chr15:50138200-50189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50144400-50159800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:50145600-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:50146400-50160000	Strong transcription	Primary hematopoietic stem cells	blood
7	chr15:50149400-50198000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:50149600-50160600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:50149600-50160800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:50156000-50168400	Weak transcription	Ovary	ovary
11	chr15:50157200-50160600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:50158400-50167800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:50158600-50160200	Weak transcription	Osteobl	bone
14	chr15:50158800-50160200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:50158800-50160200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:50158800-50160600	Enhancers	Hela-S3	cervix
17	chr15:50158800-50163600	Weak transcription	Adipose Nuclei	Adipose
18	chr15:50158800-50170600	Weak transcription	Placenta	Placenta
19	chr15:50159200-50160000	Enhancers	A549	lung
20	chr15:50159200-50160400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:50159200-50168400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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