Variant report

Variant	rs12679287
Chromosome Location	chr8:52838128-52838129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52829314..52832540-chr8:52837482..52840853,3	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10087958	0.82[JPT][hapmap]
rs10504130	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs10958300	0.96[ASN][1000 genomes]
rs10958301	0.96[ASN][1000 genomes]
rs10958305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11775587	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11775611	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777016	0.96[ASN][1000 genomes]
rs11777714	0.96[ASN][1000 genomes]
rs11778849	0.94[ASN][1000 genomes]
rs11780040	0.96[ASN][1000 genomes]
rs11781330	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs11784869	1.00[ASN][1000 genomes]
rs11785805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787229	0.90[ASN][1000 genomes]
rs12675786	0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs12675907	0.82[ASN][1000 genomes]
rs12676345	0.84[ASN][1000 genomes]
rs12676780	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12676835	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12677407	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12678639	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12679983	0.83[ASN][1000 genomes]
rs12680128	0.83[ASN][1000 genomes]
rs12681203	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12681734	0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs13265006	0.96[ASN][1000 genomes]
rs13276400	0.84[ASN][1000 genomes]
rs16916820	0.94[ASN][1000 genomes]
rs16916856	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16916865	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs16916906	0.96[ASN][1000 genomes]
rs16916961	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17212214	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17212256	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17284746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037138	0.94[ASN][1000 genomes]
rs2037139	0.96[ASN][1000 genomes]
rs2069119	0.84[ASN][1000 genomes]
rs2176120	0.96[ASN][1000 genomes]
rs34058697	0.94[ASN][1000 genomes]
rs34073804	0.85[ASN][1000 genomes]
rs34213209	0.84[ASN][1000 genomes]
rs34319820	0.85[ASN][1000 genomes]
rs34364864	0.94[ASN][1000 genomes]
rs34372756	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34677273	1.00[ASN][1000 genomes]
rs34973406	0.94[ASN][1000 genomes]
rs35032384	1.00[ASN][1000 genomes]
rs35509250	0.84[ASN][1000 genomes]
rs35603537	0.84[ASN][1000 genomes]
rs41453644	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs4292674	0.83[ASN][1000 genomes]
rs4321994	0.82[ASN][1000 genomes]
rs4534123	0.83[ASN][1000 genomes]
rs4598243	0.91[ASN][1000 genomes]
rs4626585	0.83[ASN][1000 genomes]
rs57212480	0.94[ASN][1000 genomes]
rs58561048	0.94[ASN][1000 genomes]
rs58583070	0.84[ASN][1000 genomes]
rs59602923	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60153173	0.85[ASN][1000 genomes]
rs60304457	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60796336	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61326367	0.84[ASN][1000 genomes]
rs6768	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6994203	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs71513549	0.83[ASN][1000 genomes]
rs71513552	0.85[ASN][1000 genomes]
rs71513561	0.96[ASN][1000 genomes]
rs71513564	1.00[ASN][1000 genomes]
rs763550	0.94[ASN][1000 genomes]
rs9650179	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650180	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650305	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9792352	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer 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 target site	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12679287	LOC286071	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52814000-52839200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:52814200-52842000	Weak transcription	Brain Substantia Nigra	brain
3	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
4	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
5	chr8:52822600-52860200	Weak transcription	Fetal Muscle Leg	muscle
6	chr8:52823000-52840200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr8:52823600-52838200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:52831200-52838800	Weak transcription	Left Ventricle	heart
9	chr8:52831200-52840800	Weak transcription	Right Ventricle	heart
10	chr8:52831800-52841000	Weak transcription	Lung	lung
11	chr8:52831800-52858400	Weak transcription	Primary T cells from cord blood	blood
12	chr8:52831800-52863400	Weak transcription	Aorta	Aorta
13	chr8:52832000-52838400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:52835400-52840200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr8:52837000-52838400	Enhancers	HMEC	breast
16	chr8:52837200-52838400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr8:52837200-52838400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr8:52837200-52838400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:52837800-52839200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr8:52837800-52851800	Weak transcription	Ovary	ovary
21	chr8:52838000-52839000	Weak transcription	Psoas Muscle	Psoas
22	chr8:52838000-52840800	Weak transcription	Pancreas	Pancrea
23	chr8:52838000-52853400	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links