Variant report

Variant	rs36590
Chromosome Location	chr22:30328070-30328071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1071888	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1076137	0.91[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs11090598	0.81[AMR][1000 genomes]
rs12168499	0.81[AMR][1000 genomes]
rs12168552	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12171061	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12537	0.87[CEU][hapmap]
rs131278	0.86[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.90[YRI][hapmap]
rs131291	0.84[ASW][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap]
rs131296	0.86[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs140105	0.82[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs140108	0.82[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs140135	0.86[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs140151	0.91[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs17643918	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17648725	0.81[AMR][1000 genomes]
rs1807509	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs193473	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs193481	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2017677	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2051764	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2105870	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2349225	0.91[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap]
rs2412960	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2412963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28257	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34862234	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35705048	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36578	0.86[JPT][hapmap];0.89[YRI][hapmap]
rs36580	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36586	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36596	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36598	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36604	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36606	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3887275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3958025	0.91[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs39712	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41162	0.84[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41164	0.91[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs41166	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs41172	0.87[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap]
rs41174	0.86[CEU][hapmap]
rs41175	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41177	0.83[CEU][hapmap]
rs41179	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4239932	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4239933	0.81[AMR][1000 genomes]
rs4337577	0.81[AMR][1000 genomes]
rs4820820	0.83[EUR][1000 genomes]
rs4820822	0.85[EUR][1000 genomes]
rs4823055	0.82[EUR][1000 genomes]
rs4823063	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4823070	0.81[AMR][1000 genomes]
rs4993442	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752968	0.91[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs5752986	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5752988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752993	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763630	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763644	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763674	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763675	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763680	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763689	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763691	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs715523	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718772	0.84[ASW][hapmap];0.95[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs7286070	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7292615	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737904	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs737909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737912	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7510705	0.83[AMR][1000 genomes]
rs8135823	0.81[AMR][1000 genomes]
rs8136147	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8139994	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8141404	0.95[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs8141680	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9620926	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9620943	0.83[AMR][1000 genomes]
rs9625873	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625874	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625878	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625879	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9625919	0.95[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs9625921	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1064489	chr22:30316627-30361881	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869764	chr22:30323649-30367813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs36590	MTMR3	cis	parietal	SCAN
rs36590	CRYBB3	cis	parietal	SCAN
rs36590	KIAA1671	cis	cerebellum	SCAN
rs36590	TTC28	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30311000-30333200	Weak transcription	Primary B cells from cord blood	blood
2	chr22:30311600-30343800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:30311800-30340400	Weak transcription	HSMM	muscle
4	chr22:30312600-30339800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr22:30313000-30343800	Weak transcription	Fetal Stomach	stomach
6	chr22:30313600-30339800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr22:30313600-30354200	Weak transcription	Small Intestine	intestine
8	chr22:30314200-30334200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr22:30314400-30328200	Weak transcription	Osteobl	bone
10	chr22:30314600-30329200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr22:30318000-30334000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:30319800-30329800	Weak transcription	Right Atrium	heart
13	chr22:30319800-30333800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr22:30320400-30328200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr22:30320400-30331200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr22:30320400-30333800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr22:30320600-30339800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr22:30321200-30329000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr22:30321400-30330200	Weak transcription	Left Ventricle	heart
20	chr22:30321400-30331200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr22:30321400-30339800	Weak transcription	Lung	lung
22	chr22:30321800-30334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr22:30322000-30332200	Weak transcription	Fetal Intestine Small	intestine
24	chr22:30324400-30337800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr22:30324600-30328400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr22:30325200-30328400	Weak transcription	Adipose Nuclei	Adipose
27	chr22:30326800-30330600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr22:30327000-30330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr22:30327200-30328400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr22:30327400-30328400	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr22:30327400-30328600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr22:30327600-30328400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr22:30327600-30331800	Weak transcription	Pancreas	Pancrea
34	chr22:30327600-30342200	Weak transcription	Brain Angular Gyrus	brain
35	chr22:30327800-30328200	Enhancers	GM12878-XiMat	blood
36	chr22:30327800-30328400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr22:30327800-30328400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr22:30327800-30328600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:30327800-30329600	Weak transcription	Psoas Muscle	Psoas
40	chr22:30328000-30328400	Enhancers	Colon Smooth Muscle	Colon
41	chr22:30328000-30328600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr22:30328000-30329000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr22:30328000-30329800	Weak transcription	Ovary	ovary

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