Variant report

Variant	rs12898683
Chromosome Location	chr15:31757066-31757067
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	chr15:31747904..31750478-chr15:31754531..31757245,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16956753	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs34309239	0.93[EUR][1000 genomes]
rs34560370	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34883574	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35605241	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs36114878	0.87[EUR][1000 genomes]
rs71399746	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8037258	0.93[EUR][1000 genomes]
rs877548	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1051589	chr15:31728004-31972706	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv542320	chr15:31728004-31972706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv469633	chr15:31731003-31904613	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv482330	chr15:31731003-31904613	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv903844	chr15:31736091-31781988	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1046271	chr15:31741255-31795961	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv903845	chr15:31751664-31939001	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31749200-31764000	Weak transcription	Right Atrium	heart
2	chr15:31751800-31757800	Weak transcription	A549	lung
3	chr15:31752000-31763800	Weak transcription	Primary T cells from cord blood	blood
4	chr15:31753600-31757200	Weak transcription	Hela-S3	cervix
5	chr15:31754400-31761000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:31755800-31757800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr15:31755800-31758000	Enhancers	Stomach Mucosa	stomach
8	chr15:31755800-31758200	Enhancers	Esophagus	oesophagus
9	chr15:31756400-31757200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:31756400-31757600	Enhancers	Primary B cells from peripheral blood	blood
11	chr15:31756400-31757600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr15:31756600-31757600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr15:31756600-31757800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:31756600-31757800	Enhancers	Spleen	Spleen
15	chr15:31756600-31758400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:31756600-31758400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr15:31756800-31757200	Enhancers	NHEK	skin
18	chr15:31756800-31757400	Enhancers	HMEC	breast
19	chr15:31756800-31757600	Flanking Active TSS	Colonic Mucosa	Colon
20	chr15:31756800-31757800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:31757000-31757400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr15:31757000-31757400	Enhancers	Right Ventricle	heart
23	chr15:31757000-31757600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr15:31757000-31757800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:31757000-31758200	Enhancers	Pancreas	Pancrea
26	chr15:31757000-31759600	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links