Variant report

Variant	rs2953509
Chromosome Location	chr8:87343194-87343195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:87338119..87339935-chr8:87342418..87344474,2	MCF-7	breast:
2	chr8:87341012..87343930-chr8:87343951..87346543,2	MCF-7	breast:
3	chr8:87341673..87343507-chr8:87352769..87354965,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10086340	0.85[EUR][1000 genomes]
rs10093729	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10095498	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10097450	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10098356	0.88[EUR][1000 genomes]
rs10956830	0.91[EUR][1000 genomes]
rs12541793	0.83[EUR][1000 genomes]
rs12549332	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12678720	0.85[EUR][1000 genomes]
rs12678772	0.85[EUR][1000 genomes]
rs12679811	0.83[EUR][1000 genomes]
rs13251006	0.82[EUR][1000 genomes]
rs13253261	0.83[EUR][1000 genomes]
rs13253296	0.83[EUR][1000 genomes]
rs13253515	0.83[EUR][1000 genomes]
rs13254675	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13256765	0.85[EUR][1000 genomes]
rs13258126	0.85[EUR][1000 genomes]
rs13262672	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13264364	0.83[EUR][1000 genomes]
rs13273338	0.85[EUR][1000 genomes]
rs13280468	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28378899	0.89[EUR][1000 genomes]
rs28561640	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2953510	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2953511	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2953516	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2953517	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2976177	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2976178	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2976179	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2976181	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2976201	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34227066	0.85[EUR][1000 genomes]
rs34794500	0.85[EUR][1000 genomes]
rs41469550	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4379426	0.92[EUR][1000 genomes]
rs4379427	0.84[EUR][1000 genomes]
rs4464946	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4490816	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4587306	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4623392	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4961188	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6471296	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6471309	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6471314	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6471316	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67123356	0.85[EUR][1000 genomes]
rs6992287	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6992944	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7003059	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7007855	0.91[EUR][1000 genomes]
rs7017716	0.91[EUR][1000 genomes]
rs71503461	0.80[ASN][1000 genomes]
rs7465046	0.83[ASN][1000 genomes]
rs7816275	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7820234	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7830480	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7832493	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7833049	0.85[EUR][1000 genomes]
rs7841690	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7846090	0.83[EUR][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	nsv529563	chr8:86467090-87381984	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv429926	chr8:87161695-87429872	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv3360246	chr8:87200232-87419244	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1017535	chr8:87261702-87367934	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3441725	chr8:87342885-87359895	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2953509	RMDN1	cis	Nerve Tibial	GTEx
rs2953509	RMDN1	cis	Whole Blood	GTEx
rs2953509	FAM82B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87334800-87346400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr8:87340800-87346000	Weak transcription	Liver	Liver
3	chr8:87341800-87346400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:87342600-87343400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr8:87342800-87343200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:87342800-87343600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr8:87342800-87343600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr8:87343000-87343400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr8:87343000-87343400	Enhancers	Adipose Nuclei	Adipose
10	chr8:87343000-87343400	Enhancers	Brain Germinal Matrix	brain
11	chr8:87343000-87343600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

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