Variant report

Variant	rs10181597
Chromosome Location	chr2:189954227-189954228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10178611	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10178886	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194682	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10195184	0.84[ASN][1000 genomes]
rs11686253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11690723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622083	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693526	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12693528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12989558	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13008197	0.94[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13031211	0.84[CHD][hapmap]
rs13391332	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13401377	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1356165	0.81[CHD][hapmap]
rs4667259	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6414121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434310	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434311	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434315	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434316	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434321	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434323	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7420511	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7421040	0.94[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7421525	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7423808	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7423973	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7424137	0.87[ASN][1000 genomes]
rs7424790	0.94[CEU][hapmap];0.90[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7426169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7557945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7562299	0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7568732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7576165	0.84[CHD][hapmap]
rs7602447	1.00[ASW][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7606293	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv3074	chr2:189931263-189976124	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10181597	WDR75	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189895600-189965200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:189896200-189962400	Weak transcription	Left Ventricle	heart
3	chr2:189900800-189964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:189912400-189961600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:189922800-189980800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:189933000-189960400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:189933000-189980200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:189933800-189957800	Weak transcription	Fetal Intestine Small	intestine
9	chr2:189936600-189969200	Weak transcription	Liver	Liver
10	chr2:189941200-189975000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:189942800-189961800	Weak transcription	Aorta	Aorta
12	chr2:189947200-189961200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:189947400-189958000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:189947600-189961800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:189947600-189980800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:189947800-189957000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:189948200-189957800	Weak transcription	Psoas Muscle	Psoas
18	chr2:189948200-189958000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:189948200-189959200	Weak transcription	Fetal Brain Male	brain
20	chr2:189948200-189980600	Weak transcription	Placenta	Placenta
21	chr2:189948600-189974800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:189950200-189961600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:189950800-189961400	Weak transcription	Fetal Kidney	kidney
24	chr2:189950800-189977800	Weak transcription	Fetal Intestine Large	intestine
25	chr2:189951800-189961400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:189952000-189956000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:189952000-189961600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:189952200-189956800	Strong transcription	HSMM	muscle
29	chr2:189952400-189956200	Strong transcription	NH-A	brain
30	chr2:189952600-189954400	Genic enhancers	NHDF-Ad	bronchial
31	chr2:189952600-189956000	Strong transcription	Adipose Nuclei	Adipose
32	chr2:189952800-189954800	Strong transcription	Colon Smooth Muscle	Colon
33	chr2:189952800-189955400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:189952800-189957200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:189953000-189955200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:189953400-189954400	Genic enhancers	Fetal Lung	lung
37	chr2:189953400-189954400	Genic enhancers	NHLF	lung
38	chr2:189953400-189956400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:189953400-189957000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:189953600-189955400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:189953800-189955600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr2:189953800-189955800	Strong transcription	Osteobl	bone
43	chr2:189953800-189958000	Strong transcription	A549	lung
44	chr2:189954000-189955600	Strong transcription	HSMMtube	muscle
45	chr2:189954000-189955800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:189954000-189955800	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr2:189954000-189957000	Strong transcription	Fetal Muscle Leg	muscle
48	chr2:189954200-189954400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:189954200-189954400	Enhancers	Fetal Stomach	stomach
50	chr2:189954200-189954800	Strong transcription	Ovary	ovary

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