Variant report

Variant	rs36605
Chromosome Location	chr22:30340356-30340357
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10048885	0.81[AMR][1000 genomes]
rs1071888	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1076137	0.87[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs11090598	0.81[AMR][1000 genomes]
rs12167333	0.81[AMR][1000 genomes]
rs12168499	0.81[AMR][1000 genomes]
rs12168552	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12171061	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs131278	0.82[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap]
rs131291	0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap]
rs131296	0.82[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs140135	0.82[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs140151	0.87[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap]
rs17643918	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17648725	0.81[AMR][1000 genomes]
rs1807509	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs193473	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs193481	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2017677	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2051764	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2105870	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2349225	0.87[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap]
rs2412960	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2412963	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28257	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34862234	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35705048	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36578	0.88[JPT][hapmap];0.89[YRI][hapmap]
rs36580	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36586	0.83[AMR][1000 genomes]
rs36590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36591	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36596	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36598	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36600	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36604	0.95[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36606	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788423	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3887275	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3958025	0.87[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs39712	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41162	0.91[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41164	0.87[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs41166	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41172	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs41174	0.82[CEU][hapmap]
rs41175	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41179	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4239932	0.86[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4239933	0.81[AMR][1000 genomes]
rs4337577	0.81[AMR][1000 genomes]
rs4820820	0.82[EUR][1000 genomes]
rs4820822	0.84[EUR][1000 genomes]
rs4823055	0.81[EUR][1000 genomes]
rs4823063	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4823070	0.81[AMR][1000 genomes]
rs4993442	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752968	0.86[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs5752986	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5752988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752993	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763630	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763644	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763674	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763675	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763680	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763689	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763691	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs715523	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718772	0.91[CEU][hapmap];0.84[GIH][hapmap];0.95[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];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7292615	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737904	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs737909	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737912	0.95[CEU][hapmap];0.88[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];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8139994	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8141404	0.91[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8141680	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9620926	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9620943	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9625873	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625874	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625878	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625879	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9625919	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	nsv1058511	chr22:30330447-30361881	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv2763694	chr22:30330459-30361881	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv588883	chr22:30333405-30365842	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs36605	MTMR3	cis	parietal	SCAN
rs36605	TTC28	cis	cerebellum	SCAN
rs36605	KIAA1671	cis	cerebellum	SCAN
rs36605	CRYBB3	cis	parietal	SCAN
rs36605	MTMR3	cis	multi-tissue	Pritchard

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30311600-30343800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:30311800-30340400	Weak transcription	HSMM	muscle
3	chr22:30313000-30343800	Weak transcription	Fetal Stomach	stomach
4	chr22:30313600-30354200	Weak transcription	Small Intestine	intestine
5	chr22:30327600-30342200	Weak transcription	Brain Angular Gyrus	brain
6	chr22:30328400-30343600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr22:30328400-30351800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr22:30330600-30342200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr22:30332000-30342200	Weak transcription	Gastric	stomach
10	chr22:30332600-30345000	Weak transcription	Pancreas	Pancrea
11	chr22:30332600-30347400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr22:30332800-30341000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr22:30332800-30343800	Weak transcription	Adipose Nuclei	Adipose
14	chr22:30333600-30343600	Weak transcription	Brain Anterior Caudate	brain
15	chr22:30334200-30341000	Weak transcription	Right Atrium	heart
16	chr22:30334200-30374800	Weak transcription	Thymus	Thymus
17	chr22:30334400-30341200	Weak transcription	Brain Hippocampus Middle	brain
18	chr22:30334600-30340400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr22:30334600-30341000	Weak transcription	Psoas Muscle	Psoas
20	chr22:30334600-30341000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr22:30335800-30341000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr22:30337000-30342000	Weak transcription	Brain Substantia Nigra	brain
23	chr22:30338000-30340400	Weak transcription	HSMMtube	muscle
24	chr22:30338800-30341000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr22:30339000-30343000	Weak transcription	Brain Germinal Matrix	brain
26	chr22:30339400-30341800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr22:30339800-30340400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr22:30339800-30340400	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr22:30339800-30340400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr22:30339800-30340400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr22:30339800-30340400	Enhancers	Ovary	ovary
32	chr22:30339800-30340600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr22:30339800-30340600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr22:30339800-30340800	Enhancers	Dnd41	blood
35	chr22:30339800-30341400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr22:30339800-30341800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:30339800-30342600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr22:30339800-30343200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr22:30340000-30340600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr22:30340000-30340600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr22:30340000-30340600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr22:30340000-30340600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr22:30340000-30340600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr22:30340000-30340800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr22:30340000-30340800	Enhancers	Primary T cells from cord blood	blood
46	chr22:30340000-30341000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr22:30340000-30341000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr22:30340000-30341200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr22:30340000-30341200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr22:30340000-30342600	Enhancers	Duodenum Smooth Muscle	Duodenum

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