Variant report

Variant	rs10929739
Chromosome Location	chr2:11560769-11560770
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	chr2:11560085..11562285-chr2:11564604..11566770,2	K562	blood:
2	chr2:11560712..11564441-chr2:11679547..11682198,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196208	Chromatin interaction
ENSG00000264010	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10186511	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10929736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10929737	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929740	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10929742	0.91[CEU][hapmap];0.91[JPT][hapmap]
rs11674593	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11682602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686138	0.95[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs11687178	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11687681	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11691211	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11694857	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12472962	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12611958	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12612948	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12613503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12614218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12615138	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12617534	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12990560	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12994661	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995996	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13007909	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34079430	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34313955	0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34514099	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35053846	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35090349	0.83[AMR][1000 genomes]
rs35423645	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35727311	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3922995	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4292073	0.91[CEU][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs4335920	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4553788	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4588159	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4637076	0.83[AMR][1000 genomes]
rs57197575	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61016299	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6432192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432193	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6432196	0.91[CEU][hapmap];0.91[JPT][hapmap]
rs6708001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6708015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6729114	0.80[EUR][1000 genomes]
rs6735687	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6735707	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6736082	0.83[ASN][1000 genomes]
rs6736199	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743597	0.83[ASN][1000 genomes]
rs6750266	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750482	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750499	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751915	0.95[CEU][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7595697	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9789694	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11546600-11584200	Weak transcription	Pancreas	Pancrea
2	chr2:11552600-11561000	Weak transcription	Psoas Muscle	Psoas
3	chr2:11559000-11561400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:11559800-11561000	Enhancers	Fetal Heart	heart
5	chr2:11560000-11561000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:11560000-11561200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:11560000-11561200	Enhancers	Adipose Nuclei	Adipose
8	chr2:11560200-11561000	Weak transcription	Left Ventricle	heart
9	chr2:11560400-11561200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:11560400-11561200	Enhancers	HSMMtube	muscle
11	chr2:11560400-11562800	Weak transcription	Right Ventricle	heart
12	chr2:11560400-11563000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr2:11560400-11584000	Weak transcription	Aorta	Aorta
14	chr2:11560600-11560800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:11560600-11561200	Enhancers	NHDF-Ad	bronchial
16	chr2:11560600-11561800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr2:11560600-11563600	Enhancers	Ovary	ovary
18	chr2:11560600-11576800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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