Variant report

Variant	rs11175593
Chromosome Location	chr12:40601940-40601941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10506143	1.00[JPT][hapmap]
rs10506144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs10506146	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10506147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506154	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10878244	1.00[JPT][hapmap]
rs11174697	0.87[EUR][1000 genomes]
rs11175186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11564107	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11564117	1.00[AFR][1000 genomes]
rs11564123	1.00[JPT][hapmap]
rs11564131	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11564152	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11564153	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564185	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11564187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564190	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11564196	1.00[JPT][hapmap]
rs11564199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11564209	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11564210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564212	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564214	1.00[AFR][1000 genomes]
rs11564216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11564218	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11564256	1.00[CEU][hapmap]
rs11564266	1.00[CEU][hapmap]
rs11564271	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs12422544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12422796	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs12423419	1.00[JPT][hapmap]
rs12423551	1.00[JPT][hapmap]
rs12424040	0.93[EUR][1000 genomes]
rs12424294	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12425561	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12426378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs12426639	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12426643	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12426903	1.00[CEU][hapmap]
rs12427022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12427245	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs1365768	1.00[CEU][hapmap]
rs1365769	1.00[CEU][hapmap]
rs1388585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1388597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463717	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs1491945	0.90[AMR][1000 genomes]
rs17442924	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443078	0.86[EUR][1000 genomes]
rs17443178	0.80[EUR][1000 genomes]
rs17443185	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443206	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443600	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs17443656	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs17443909	0.87[EUR][1000 genomes]
rs17444028	0.94[EUR][1000 genomes]
rs17444054	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs17444103	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17444646	1.00[CEU][hapmap]
rs17444667	1.00[CEU][hapmap]
rs17458230	1.00[JPT][hapmap]
rs17458549	0.93[EUR][1000 genomes]
rs17458808	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17461387	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17461575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461664	0.94[EUR][1000 genomes]
rs17465610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17465946	0.87[EUR][1000 genomes]
rs17466016	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs17466626	1.00[CEU][hapmap]
rs17466907	1.00[CEU][hapmap]
rs17466969	1.00[CEU][hapmap]
rs17467039	1.00[CEU][hapmap]
rs17483919	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17484003	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17484141	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs17484342	0.94[EUR][1000 genomes]
rs17484493	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2017917	1.00[CEU][hapmap]
rs2131081	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2638223	0.86[EUR][1000 genomes]
rs2708460	0.86[EUR][1000 genomes]
rs28365169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs28365173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs28365206	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28365229	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs28365689	0.93[EUR][1000 genomes]
rs28370649	0.80[EUR][1000 genomes]
rs28370650	0.80[EUR][1000 genomes]
rs28370664	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs28370682	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs28370830	0.87[EUR][1000 genomes]
rs36212067	0.94[EUR][1000 genomes]
rs36220738	0.94[EUR][1000 genomes]
rs3789329	1.00[CEU][hapmap]
rs3899331	1.00[CEU][hapmap]
rs4628750	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs4767962	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4767964	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4767965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4768226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4768228	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs4768248	1.00[CEU][hapmap]
rs4768249	1.00[CEU][hapmap]
rs4768251	1.00[CEU][hapmap]
rs72547977	0.87[EUR][1000 genomes]
rs729215	0.93[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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease	18587394	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11175593	ARL9	trans	brain	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40597200-40602200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:40597200-40602200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:40597200-40602200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:40600200-40602200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:40600200-40602400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:40601000-40602000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:40601200-40602000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:40601200-40602000	Enhancers	NHEK	skin
9	chr12:40601200-40602600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:40601400-40604400	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:40601600-40602000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:40601600-40602000	Enhancers	Hela-S3	cervix
13	chr12:40601600-40604400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr12:40601800-40602200	Enhancers	Primary B cells from cord blood	blood
15	chr12:40601800-40602400	Weak transcription	A549	lung
16	chr12:40601800-40602600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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