Variant report

Variant	rs2088164
Chromosome Location	chr15:45792777-45792778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10152697	0.86[CHB][hapmap]
rs10851425	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1153829	0.93[JPT][hapmap]
rs1153830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1153831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1153832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1288861	0.88[CHB][hapmap]
rs1288863	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1288865	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16944629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16952731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17535381	0.88[CHB][hapmap]
rs17537244	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[TSI][hapmap]
rs1768458	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2433600	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];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2433617	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2433619	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2486287	0.88[CHB][hapmap]
rs35828336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4448883	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55997350	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56179992	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56405528	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59574269	0.85[EUR][1000 genomes]
rs60350201	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60992352	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61193305	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493154	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6493158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493160	0.88[EUR][1000 genomes]
rs7165838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7169748	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7170090	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap]
rs7171406	0.88[EUR][1000 genomes]
rs7173983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72711264	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72711278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711280	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711283	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711284	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72711290	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72711294	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72711301	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72713103	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72713104	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72713105	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8023437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025407	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8029509	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8040466	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9972498	0.88[CHB][hapmap];1.00[MEX][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	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1045556	chr15:45777396-45884854	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2088164	GPR176	cis	cerebellum	SCAN
rs2088164	TMEM62	cis	cerebellum	SCAN
rs2088164	SLC30A4	cis	parietal	SCAN
rs2088164	RPAP1	cis	cerebellum	SCAN
rs2088164	MGA	cis	parietal	SCAN
rs2088164	FAM82A2	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45751200-45801600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:45754200-45801600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:45757000-45794600	Weak transcription	Colonic Mucosa	Colon
4	chr15:45757000-45801800	Weak transcription	Gastric	stomach
5	chr15:45767200-45813600	Weak transcription	Psoas Muscle	Psoas
6	chr15:45769200-45812000	Weak transcription	Small Intestine	intestine
7	chr15:45769400-45794600	Weak transcription	Fetal Intestine Small	intestine
8	chr15:45769400-45794800	Weak transcription	Ovary	ovary
9	chr15:45769400-45813000	Weak transcription	Fetal Intestine Large	intestine
10	chr15:45769800-45794600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr15:45771000-45813400	Weak transcription	Right Ventricle	heart
12	chr15:45771200-45814000	Weak transcription	Placenta	Placenta
13	chr15:45772000-45801600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr15:45773200-45814000	Weak transcription	Pancreas	Pancrea
15	chr15:45774600-45812800	Weak transcription	Fetal Brain Male	brain
16	chr15:45775600-45812800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr15:45776000-45800400	Weak transcription	Esophagus	oesophagus
18	chr15:45778000-45813000	Weak transcription	Brain Germinal Matrix	brain
19	chr15:45778400-45801800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:45778400-45812600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:45778800-45806400	Weak transcription	Spleen	Spleen
22	chr15:45779400-45812800	Weak transcription	Fetal Brain Female	brain
23	chr15:45779800-45799800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:45779800-45800200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:45780000-45800000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:45780000-45800000	Weak transcription	Liver	Liver
27	chr15:45780200-45794600	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:45780400-45794600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:45780400-45800200	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:45781200-45800200	Weak transcription	Brain Substantia Nigra	brain
31	chr15:45781200-45801800	Weak transcription	Aorta	Aorta
32	chr15:45781600-45797800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:45781800-45793600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:45781800-45794600	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:45781800-45798400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:45781800-45800000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:45781800-45800000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:45781800-45800000	Weak transcription	Fetal Lung	lung
39	chr15:45781800-45800400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:45781800-45801400	Weak transcription	Primary T cells from cord blood	blood
41	chr15:45781800-45801800	Weak transcription	Lung	lung
42	chr15:45781800-45802400	Weak transcription	Primary B cells from cord blood	blood
43	chr15:45782000-45797000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr15:45782000-45800200	Weak transcription	Left Ventricle	heart
45	chr15:45782600-45800000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr15:45783800-45793800	Weak transcription	Fetal Stomach	stomach
47	chr15:45783800-45800000	Weak transcription	Adipose Nuclei	Adipose
48	chr15:45783800-45812800	Weak transcription	Fetal Kidney	kidney
49	chr15:45784000-45800000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:45788000-45812800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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