Variant report

Variant	rs2170427
Chromosome Location	chr4:87566027-87566028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10516775	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10516776	1.00[CEU][hapmap];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[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011956	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011965	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.87[YRI][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];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011984	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011988	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012007	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012012	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];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs17454369	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2200052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2219993	1.00[CEU][hapmap];0.87[YRI][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[AFR][1000 genomes];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[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4604024	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627823	0.87[EUR][1000 genomes]
rs61121590	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7690137	0.87[EUR][1000 genomes]
rs980637	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980638	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv879523	chr4:87517609-87594472	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv879524	chr4:87517609-87603929	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv2755470	chr4:87536515-87613212	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87541200-87571200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87542800-87566400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:87544400-87571200	Weak transcription	Pancreas	Pancrea
4	chr4:87546200-87569400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:87554600-87567000	Weak transcription	Osteobl	bone
6	chr4:87554600-87567400	Weak transcription	Esophagus	oesophagus
7	chr4:87555800-87567600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:87555800-87567800	Weak transcription	Fetal Intestine Large	intestine
9	chr4:87556200-87570800	Weak transcription	Fetal Stomach	stomach
10	chr4:87557600-87567800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:87557600-87569200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:87557600-87569600	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:87557600-87571000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:87557600-87571200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:87557800-87567800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:87557800-87568200	Weak transcription	Fetal Kidney	kidney
17	chr4:87557800-87568400	Weak transcription	Brain Substantia Nigra	brain
18	chr4:87557800-87568800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:87557800-87569000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:87557800-87569400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:87557800-87569400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:87557800-87569400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:87557800-87569600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:87557800-87569600	Weak transcription	Fetal Lung	lung
25	chr4:87557800-87570200	Weak transcription	Ovary	ovary
26	chr4:87558000-87568600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:87561000-87570000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:87561600-87566800	Weak transcription	HMEC	breast
29	chr4:87561800-87569600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:87562000-87566200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:87562400-87566400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:87563000-87568800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:87563000-87571000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:87563800-87568600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:87563800-87569800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:87564400-87570800	Weak transcription	Fetal Intestine Small	intestine
37	chr4:87565200-87566600	Strong transcription	NHEK	skin
38	chr4:87565400-87566400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:87565400-87566600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:87565600-87566600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:87566000-87566400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:87566000-87566600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:87566000-87567000	Strong transcription	NHDF-Ad	bronchial

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