Variant report

Variant	rs13090949
Chromosome Location	chr3:105516223-105516224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11919893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11926659	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12486371	0.83[CEU][hapmap]
rs12496588	0.84[CEU][hapmap]
rs12497428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326550	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13433776	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1503923	0.81[ASN][1000 genomes]
rs16851596	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851705	0.86[ASN][1000 genomes]
rs16851706	0.83[ASN][1000 genomes]
rs2120103	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2120104	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2399056	0.92[CEU][hapmap]
rs3772512	0.80[CEU][hapmap]
rs6437616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776593	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778745	0.83[CEU][hapmap]
rs6780432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6791765	0.83[CEU][hapmap]
rs7634195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639888	0.83[CEU][hapmap]
rs894541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9811776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9837243	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846445	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849559	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9872895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876110	0.83[CEU][hapmap]
rs9880744	0.84[CEU][hapmap]

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	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
3	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
4	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:105495400-105517200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:105501800-105516600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
8	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:105505600-105517400	Weak transcription	Brain Substantia Nigra	brain
10	chr3:105506600-105518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:105509800-105527800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:105510000-105517400	Weak transcription	Stomach Mucosa	stomach
13	chr3:105510200-105516400	Weak transcription	Primary T cells from cord blood	blood
14	chr3:105510600-105521200	Weak transcription	Fetal Brain Male	brain
15	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
16	chr3:105511600-105516600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:105511600-105516800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:105511800-105520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:105512000-105516800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:105512000-105516800	Weak transcription	NH-A	brain
21	chr3:105512000-105520600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:105512200-105516600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:105512200-105517200	Weak transcription	Fetal Lung	lung
24	chr3:105512200-105517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:105512200-105517400	Weak transcription	Fetal Heart	heart
26	chr3:105512200-105517400	Weak transcription	Ovary	ovary
27	chr3:105512200-105517400	Weak transcription	Small Intestine	intestine
28	chr3:105512200-105519000	Weak transcription	Psoas Muscle	Psoas
29	chr3:105512200-105519000	Weak transcription	Right Atrium	heart
30	chr3:105512200-105519200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:105512200-105520200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:105512200-105520400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:105512200-105527200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart
35	chr3:105512400-105524400	Weak transcription	NHLF	lung
36	chr3:105512600-105516800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:105512600-105518200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:105512600-105520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:105512600-105524000	Weak transcription	HSMMtube	muscle
40	chr3:105512600-105524600	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:105512600-105525200	Weak transcription	HSMM	muscle
42	chr3:105512800-105517400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:105512800-105517400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:105512800-105517400	Weak transcription	A549	lung
45	chr3:105513000-105516400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:105513400-105517200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:105513400-105517200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:105513400-105517800	Weak transcription	Osteobl	bone
49	chr3:105513600-105516600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:105513800-105517200	Weak transcription	NHDF-Ad	bronchial

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