Variant report

Variant	rs7863476
Chromosome Location	chr9:26915925-26915926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10511793	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs10738762	0.88[ASW][hapmap];0.84[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10757634	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10757635	0.82[ASW][hapmap];0.84[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10757636	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10812479	0.87[EUR][1000 genomes]
rs10812482	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10812487	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10812488	0.88[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10812490	0.80[ASN][1000 genomes]
rs10812491	0.80[ASN][1000 genomes]
rs10812492	0.84[TSI][hapmap]
rs10812494	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs10812503	0.90[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10812504	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10812507	0.90[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10812518	0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap]
rs10967548	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10967549	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10967551	0.84[EUR][1000 genomes]
rs10967556	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10967586	0.89[JPT][hapmap]
rs10967594	0.88[TSI][hapmap]
rs10967652	0.90[CEU][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10967679	0.94[JPT][hapmap]
rs12337896	0.88[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.82[AMR][1000 genomes]
rs12342005	0.82[CEU][hapmap]
rs12345197	0.81[AMR][1000 genomes]
rs1541144	0.90[CEU][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3758218	0.90[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4316229	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4413873	0.90[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4621911	0.94[JPT][hapmap]
rs59159685	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62544398	0.81[EUR][1000 genomes]
rs6475944	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6475945	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6475946	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6475947	0.94[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6475948	0.81[TSI][hapmap]
rs6475954	0.94[JPT][hapmap]
rs7018585	0.90[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs7020010	0.84[JPT][hapmap]
rs7032756	0.94[ASW][hapmap];0.89[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs7033238	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7034478	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7034670	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7035292	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038218	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7040505	0.82[AMR][1000 genomes]
rs7042133	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7042447	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7849248	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs7856462	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7857481	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7857669	0.88[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap]
rs7860542	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7868158	0.83[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7870787	0.84[JPT][hapmap]
rs7871097	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs7871286	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs7871668	0.94[JPT][hapmap]
rs7872496	0.89[JPT][hapmap]
rs7875068	0.90[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]

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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7863476	IFT74	cis	parietal	SCAN
rs7863476	IFT74	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26892800-26916200	Weak transcription	Small Intestine	intestine
2	chr9:26893000-26916000	Weak transcription	Left Ventricle	heart
3	chr9:26893000-26916000	Weak transcription	Pancreas	Pancrea
4	chr9:26893000-26916200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:26893000-26922600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:26893000-26924200	Weak transcription	Esophagus	oesophagus
7	chr9:26893200-26923200	Weak transcription	Right Ventricle	heart
8	chr9:26893400-26916000	Weak transcription	Fetal Lung	lung
9	chr9:26893400-26916800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:26893400-26925000	Weak transcription	Stomach Mucosa	stomach
11	chr9:26893400-26936400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:26893400-26936400	Weak transcription	Psoas Muscle	Psoas
13	chr9:26893600-26916000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:26893600-26916000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:26893600-26916000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:26898200-26924400	Weak transcription	Aorta	Aorta
17	chr9:26899200-26921200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr9:26899400-26916200	Weak transcription	NHEK	skin
19	chr9:26900600-26916200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:26900800-26930000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:26901200-26935800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:26901600-26916000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:26901600-26920800	Weak transcription	Gastric	stomach
24	chr9:26902800-26936600	Weak transcription	Spleen	Spleen
25	chr9:26903000-26927800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:26903000-26929800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:26903000-26935200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr9:26903200-26928400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:26903200-26930000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:26903200-26932600	Strong transcription	Dnd41	blood
31	chr9:26903200-26935200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr9:26903800-26927800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:26903800-26931600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr9:26904600-26935200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:26904800-26916200	Weak transcription	Fetal Heart	heart
36	chr9:26905400-26938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:26905800-26937400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr9:26906000-26916000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:26906000-26916000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr9:26906000-26916000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr9:26906000-26916200	Weak transcription	HSMMtube	muscle
42	chr9:26906000-26916800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr9:26906000-26921200	Weak transcription	Fetal Brain Male	brain
44	chr9:26906200-26916200	Weak transcription	Brain Substantia Nigra	brain
45	chr9:26906200-26916200	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:26906200-26928800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:26906200-26936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr9:26907000-26916000	Weak transcription	Ovary	ovary
49	chr9:26907000-26916000	Weak transcription	HMEC	breast
50	chr9:26907400-26916000	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links