Variant report

Variant	rs11126378
Chromosome Location	chr2:72901384-72901385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10180259	0.87[EUR][1000 genomes]
rs10496185	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs10496187	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11126369	0.85[CEU][hapmap];0.82[YRI][hapmap]
rs11126382	0.88[AFR][1000 genomes]
rs11126386	0.88[AFR][1000 genomes]
rs11689339	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11689707	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs11884266	0.92[CEU][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11892598	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs12614041	0.81[AFR][1000 genomes]
rs12615875	0.81[AFR][1000 genomes]
rs12619068	0.88[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12619565	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs1562361	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17008241	1.00[CEU][hapmap]
rs17008293	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs17008315	0.92[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17008360	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs17008369	0.85[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17008371	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17263172	0.85[CEU][hapmap]
rs1876488	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2068410	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs4597553	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs4852292	0.85[YRI][hapmap]
rs4852896	0.80[AFR][1000 genomes]
rs55642420	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56058174	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57192957	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58890506	0.89[AFR][1000 genomes]
rs59216875	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60284189	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60314340	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60584321	0.80[AFR][1000 genomes]
rs61619102	0.89[AFR][1000 genomes]
rs61736520	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6546777	0.81[YRI][hapmap]
rs66469454	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66509842	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66794803	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6713143	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6713712	1.00[CEU][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6716335	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6720889	0.85[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs6736649	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6739768	1.00[CEU][hapmap]
rs6740390	1.00[CEU][hapmap]
rs6749495	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6756070	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs6761253	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs67869181	0.90[EUR][1000 genomes]
rs67926386	0.86[EUR][1000 genomes]
rs67927720	0.85[AFR][1000 genomes]
rs7565198	0.81[YRI][hapmap]
rs7586886	0.83[AFR][1000 genomes]
rs7591025	0.81[YRI][hapmap]
rs7593084	0.89[ASW][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7604083	1.00[CEU][hapmap]
rs7604402	0.88[YRI][hapmap]
rs7604818	0.93[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs7607226	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs764766	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11126378	TGFA	cis	cerebellum	SCAN
rs11126378	AUP1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72858400-72904000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:72866800-72902600	Weak transcription	Left Ventricle	heart
3	chr2:72873000-72903800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:72892000-72905400	Weak transcription	Pancreas	Pancrea
5	chr2:72895400-72902600	Weak transcription	Fetal Lung	lung
6	chr2:72895800-72903400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:72896000-72905400	Weak transcription	Psoas Muscle	Psoas
8	chr2:72896800-72903800	Weak transcription	NHEK	skin
9	chr2:72896800-72943000	Weak transcription	Primary T cells from cord blood	blood
10	chr2:72897000-72903400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:72897000-72903400	Weak transcription	NHDF-Ad	bronchial
12	chr2:72897000-72904000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:72897000-72905200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:72897000-72912600	Weak transcription	NHLF	lung
15	chr2:72897200-72902200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:72897800-72909800	Weak transcription	Brain Germinal Matrix	brain
17	chr2:72899400-72903400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:72899400-72905400	Weak transcription	Right Ventricle	heart
19	chr2:72900000-72903400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:72900000-72905400	Weak transcription	Small Intestine	intestine
21	chr2:72900200-72901400	Enhancers	HepG2	liver
22	chr2:72900200-72902200	Weak transcription	Liver	Liver
23	chr2:72900200-72911800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:72900400-72901400	Enhancers	Fetal Heart	heart
25	chr2:72900400-72901800	Enhancers	Fetal Intestine Large	intestine
26	chr2:72900400-72901800	Enhancers	Stomach Mucosa	stomach
27	chr2:72900600-72902600	Weak transcription	Ovary	ovary
28	chr2:72900600-72903000	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:72900800-72901600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:72900800-72903400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:72901000-72901600	Flanking Active TSS	A549	lung
32	chr2:72901200-72901600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:72901200-72902000	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links