Variant report

Variant	rs10516776
Chromosome Location	chr4:87623131-87623132
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	chr4:87617245..87619402-chr4:87619927..87623760,3	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10516775	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1344260	0.87[EUR][1000 genomes]
rs17011953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011954	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011956	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011959	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011965	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011966	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011968	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011978	1.00[CEU][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011984	1.00[CEU][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011988	1.00[CEU][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012007	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012018	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17419783	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17454077	0.82[CEU][hapmap]
rs17454369	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2170427	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2200052	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2219993	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648374	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28653505	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2869442	0.87[EUR][1000 genomes]
rs2869443	0.87[EUR][1000 genomes]
rs2904103	0.87[EUR][1000 genomes]
rs34155193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35434858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4561893	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4604024	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627823	0.87[EUR][1000 genomes]
rs61121590	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61344492	0.87[EUR][1000 genomes]
rs72870675	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72872208	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72872209	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7690137	0.87[EUR][1000 genomes]
rs980637	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980638	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS 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 miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87574600-87644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87579200-87642600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:87579400-87644400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:87586400-87643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:87591800-87639000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:87591800-87641000	Weak transcription	Brain Anterior Caudate	brain
7	chr4:87592400-87627800	Weak transcription	HMEC	breast
8	chr4:87592400-87656400	Weak transcription	Adipose Nuclei	Adipose
9	chr4:87593800-87641400	Weak transcription	Brain Angular Gyrus	brain
10	chr4:87594400-87642600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:87594400-87659800	Weak transcription	Ovary	ovary
12	chr4:87594800-87639200	Weak transcription	Fetal Kidney	kidney
13	chr4:87595200-87638200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:87595200-87651200	Weak transcription	Fetal Stomach	stomach
15	chr4:87600400-87639200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:87604800-87638200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:87605000-87624800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:87606600-87624800	Weak transcription	Esophagus	oesophagus
19	chr4:87606800-87641000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:87609800-87625400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:87610400-87639600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:87611400-87624600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:87611400-87627800	Weak transcription	NHEK	skin
24	chr4:87611400-87638200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:87611800-87623200	Weak transcription	NHDF-Ad	bronchial
26	chr4:87618800-87624400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:87619200-87626400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:87619400-87625800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:87622000-87623400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:87622200-87623400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:87622200-87623400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:87622200-87623400	Strong transcription	Fetal Lung	lung
33	chr4:87622400-87623400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:87622400-87623400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:87622400-87623600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:87622600-87623400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:87622600-87623400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:87622600-87623600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:87622600-87629800	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:87622800-87623600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:87623000-87628000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links