Variant report

Variant	rs16972499
Chromosome Location	chr15:42325758-42325759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42318244..42322022-chr15:42323761..42326594,4	K562	blood:
2	chr15:42281486..42282251-chr15:42325577..42326393,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11632564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11632634	0.89[ASN][1000 genomes]
rs16972456	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs16972467	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs16972470	0.84[ASN][1000 genomes]
rs16972493	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16972496	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16972507	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2412654	0.98[ASN][1000 genomes]
rs2412655	0.98[ASN][1000 genomes]
rs28422161	0.88[ASN][1000 genomes]
rs28460654	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28526333	0.89[ASN][1000 genomes]
rs55845751	0.84[ASN][1000 genomes]
rs55971911	0.84[ASN][1000 genomes]
rs66843757	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7175498	0.84[ASN][1000 genomes]
rs7176399	0.84[ASN][1000 genomes]
rs7179219	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7182355	0.84[ASN][1000 genomes]
rs73397815	0.84[ASN][1000 genomes]
rs73397843	0.95[ASN][1000 genomes]
rs7496336	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs8029818	0.91[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv569235	chr15:42304628-42326259	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv904130	chr15:42323591-42336018	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42320400-42327200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:42322000-42327200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:42324000-42326200	Enhancers	Psoas Muscle	Psoas
4	chr15:42324200-42326600	Weak transcription	NHEK	skin
5	chr15:42324200-42327800	Enhancers	Esophagus	oesophagus
6	chr15:42324600-42325800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr15:42325000-42325800	Weak transcription	HMEC	breast
8	chr15:42325200-42325800	Weak transcription	Lung	lung
9	chr15:42325200-42326000	Enhancers	Colonic Mucosa	Colon
10	chr15:42325200-42326200	Weak transcription	HepG2	liver
11	chr15:42325200-42327200	Weak transcription	Placenta	Placenta
12	chr15:42325400-42326200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr15:42325400-42326600	Enhancers	GM12878-XiMat	blood
14	chr15:42325400-42327200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:42325400-42328400	Weak transcription	Right Ventricle	heart
16	chr15:42325400-42328800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:42325600-42326000	Enhancers	Primary B cells from peripheral blood	blood
18	chr15:42325600-42327200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:42325600-42327200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:42325600-42327600	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links