Variant report

Variant	rs41162
Chromosome Location	chr22:30408710-30408711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1071888	0.82[EUR][1000 genomes]
rs1076137	0.87[CEU][hapmap]
rs12168552	0.83[EUR][1000 genomes]
rs12171061	0.85[EUR][1000 genomes]
rs17643918	0.85[EUR][1000 genomes]
rs1807509	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs193473	0.85[EUR][1000 genomes]
rs193481	0.86[EUR][1000 genomes]
rs2017677	0.93[EUR][1000 genomes]
rs2051764	0.93[EUR][1000 genomes]
rs2412960	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412963	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs28257	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34862234	0.85[EUR][1000 genomes]
rs35705048	0.83[EUR][1000 genomes]
rs36578	0.89[YRI][hapmap]
rs36580	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36590	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36591	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36594	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36596	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36598	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36600	0.82[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36601	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36604	0.82[ASW][hapmap];0.95[CEU][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36605	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36606	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36607	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3788423	0.84[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3887275	0.95[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3958025	0.82[ASW][hapmap];0.87[CEU][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap]
rs39712	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41164	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41166	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41172	0.87[CEU][hapmap];0.87[TSI][hapmap]
rs41174	0.91[CEU][hapmap]
rs41175	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41177	0.80[CEU][hapmap]
rs41179	0.85[EUR][1000 genomes]
rs4239932	0.84[ASW][hapmap];0.95[CEU][hapmap];0.81[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4823063	0.95[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4993442	0.82[EUR][1000 genomes]
rs5752968	0.86[CEU][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap]
rs5752986	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5752988	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5752993	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5763630	0.89[EUR][1000 genomes]
rs5763634	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5763644	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5763674	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5763675	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5763680	0.93[EUR][1000 genomes]
rs5763689	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5763691	0.82[EUR][1000 genomes]
rs715523	0.92[EUR][1000 genomes]
rs718772	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs7286070	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7292615	0.85[EUR][1000 genomes]
rs737904	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs737909	0.95[CEU][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs737912	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8136147	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8139994	0.84[EUR][1000 genomes]
rs8141404	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs8141680	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs9614162	0.85[MKK][hapmap];0.82[YRI][hapmap]
rs9620926	0.85[EUR][1000 genomes]
rs9620943	0.82[EUR][1000 genomes]
rs9625873	0.86[EUR][1000 genomes]
rs9625874	0.86[EUR][1000 genomes]
rs9625878	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9625879	0.83[EUR][1000 genomes]
rs9625919	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9625921	0.80[CEU][hapmap]

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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs41162	MTMR3	cis	parietal	SCAN
rs41162	KIAA1671	cis	cerebellum	SCAN
rs41162	TTC28	cis	cerebellum	SCAN
rs41162	CRYBB3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr22:30389200-30409200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:30389200-30411600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:30389200-30411800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr22:30391200-30411400	Weak transcription	Small Intestine	intestine
8	chr22:30391400-30409800	Weak transcription	Fetal Heart	heart
9	chr22:30391400-30411600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr22:30391600-30409800	Weak transcription	K562	blood
12	chr22:30391600-30417800	Weak transcription	Right Atrium	heart
13	chr22:30392600-30425000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr22:30393800-30424800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr22:30394600-30424600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr22:30394800-30425200	Strong transcription	Fetal Intestine Large	intestine
17	chr22:30394800-30426200	Strong transcription	Placenta	Placenta
18	chr22:30396800-30426200	Strong transcription	Primary B cells from cord blood	blood
19	chr22:30397600-30419800	Strong transcription	Dnd41	blood
20	chr22:30397800-30423800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr22:30397800-30425400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr22:30398000-30424400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr22:30398000-30426200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr22:30398200-30410400	Strong transcription	HSMM	muscle
25	chr22:30398400-30425000	Strong transcription	Primary hematopoietic stem cells	blood
26	chr22:30398600-30425200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr22:30399600-30415400	Weak transcription	A549	lung
28	chr22:30399800-30422400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr22:30401200-30420000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr22:30401200-30423200	Strong transcription	Adipose Nuclei	Adipose
31	chr22:30401400-30411600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr22:30401600-30425200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr22:30401800-30410200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr22:30401800-30411800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr22:30402000-30422600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr22:30402000-30422600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr22:30402200-30425200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr22:30402400-30420800	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr22:30402400-30424600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr22:30402600-30410600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr22:30402600-30411000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr22:30402600-30411000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr22:30402600-30423600	Strong transcription	Liver	Liver
44	chr22:30402600-30426200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr22:30402800-30409800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr22:30402800-30424200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr22:30402800-30425800	Strong transcription	Fetal Muscle Leg	muscle
48	chr22:30403000-30409800	Strong transcription	HSMMtube	muscle
49	chr22:30403000-30410200	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr22:30403000-30411600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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