Variant report

Variant	rs60517889
Chromosome Location	chr3:160266347-160266348
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2305401	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305406	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs33999879	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3736627	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773371	0.86[EUR][1000 genomes]
rs3806629	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41272959	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56124988	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56343019	0.95[ASN][1000 genomes]
rs56396435	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56401539	0.84[EUR][1000 genomes]
rs57030267	1.00[AMR][1000 genomes]
rs57050097	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57277659	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57285344	0.85[AMR][1000 genomes]
rs57328745	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57555307	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58377812	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58654032	1.00[AMR][1000 genomes]
rs58776572	0.84[EUR][1000 genomes]
rs58915028	1.00[AMR][1000 genomes]
rs59695030	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59799252	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60066272	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60153357	1.00[AMR][1000 genomes]
rs60607858	0.84[EUR][1000 genomes]
rs60914777	0.85[AMR][1000 genomes]
rs61066536	1.00[AMR][1000 genomes]
rs62272179	0.85[AMR][1000 genomes]
rs62272187	0.85[AMR][1000 genomes]
rs62272188	0.85[AMR][1000 genomes]
rs62272190	0.85[AMR][1000 genomes]
rs62272191	0.85[AMR][1000 genomes]
rs62272193	0.85[AMR][1000 genomes]
rs62272196	1.00[AMR][1000 genomes]
rs62272198	1.00[AMR][1000 genomes]
rs62272231	1.00[AMR][1000 genomes]
rs62272236	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62272237	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62272243	0.84[AMR][1000 genomes]
rs62272245	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62272247	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62272249	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62272251	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62272253	0.84[AMR][1000 genomes]
rs62272254	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272255	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272256	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272257	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272258	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272259	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272780	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272781	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272783	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272785	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272787	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272788	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272790	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272793	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62272799	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62272804	0.95[ASN][1000 genomes]
rs62272805	0.95[ASN][1000 genomes]
rs62272806	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272831	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272833	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272836	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272838	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66850724	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67403526	0.90[ASN][1000 genomes]
rs68069205	0.86[EUR][1000 genomes]
rs73154564	0.84[AMR][1000 genomes]
rs73154582	0.92[AMR][1000 genomes]
rs73154587	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73155914	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645798	0.81[EUR][1000 genomes]
rs7648832	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
8	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
2	chr3:160235000-160266600	Weak transcription	Esophagus	oesophagus
3	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:160244200-160272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:160246600-160279200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:160246800-160266400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:160247000-160270400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
9	chr3:160248800-160268600	Weak transcription	NHLF	lung
10	chr3:160249200-160279000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:160250400-160271600	Weak transcription	HepG2	liver
12	chr3:160251000-160266800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:160251200-160282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:160252400-160267200	Weak transcription	Primary B cells from cord blood	blood
15	chr3:160252800-160272600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:160253000-160267400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:160253000-160272000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:160253400-160268000	Weak transcription	Liver	Liver
19	chr3:160253600-160267800	Weak transcription	NHEK	skin
20	chr3:160254000-160272600	Weak transcription	Hela-S3	cervix
21	chr3:160254000-160279800	Weak transcription	Placenta	Placenta
22	chr3:160254200-160267400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:160254200-160268000	Weak transcription	Fetal Intestine Large	intestine
24	chr3:160254200-160278800	Weak transcription	HMEC	breast
25	chr3:160256600-160267400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:160258600-160273800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:160258800-160279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:160259000-160269200	Weak transcription	NH-A	brain
29	chr3:160259200-160277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:160259800-160272600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:160260200-160268200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:160260200-160271400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:160260200-160279600	Weak transcription	Osteobl	bone
34	chr3:160260400-160266800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:160260400-160268400	Weak transcription	NHDF-Ad	bronchial
36	chr3:160260600-160268000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:160260600-160271000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:160261000-160267200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr3:160261000-160271400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:160261800-160267200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:160261800-160281000	Weak transcription	Ovary	ovary
42	chr3:160262000-160267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:160262000-160268000	Weak transcription	Fetal Stomach	stomach
44	chr3:160262000-160272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:160262600-160266600	Weak transcription	A549	lung
46	chr3:160262600-160277800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:160263000-160267400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:160263200-160268400	Weak transcription	Fetal Kidney	kidney
49	chr3:160263600-160267200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:160263600-160270400	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links