Variant report

Variant	rs2433600
Chromosome Location	chr15:45776424-45776425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

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];0.96[EUR][1000 genomes];0.92[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];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1153832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[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];0.83[EUR][1000 genomes];0.85[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	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2088164	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	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2433619	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2486287	0.88[CHB][hapmap]
rs35828336	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55997350	0.89[AMR][1000 genomes]
rs56179992	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56405528	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60350201	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60992352	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61193305	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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];0.89[EUR][1000 genomes];0.85[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];0.82[EUR][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];0.82[EUR][1000 genomes]
rs6493160	0.81[EUR][1000 genomes]
rs7165838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7169748	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7170090	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap]
rs7171406	0.81[EUR][1000 genomes]
rs7173983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs72711264	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72711278	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72711279	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72711280	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72711283	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72711284	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72711290	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72711294	0.82[EUR][1000 genomes]
rs72711301	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72713103	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72713104	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72713105	0.83[AMR][1000 genomes];0.81[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];0.85[EUR][1000 genomes];0.82[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];0.82[EUR][1000 genomes]
rs8029509	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8040466	0.88[EUR][1000 genomes];0.85[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];0.82[EUR][1000 genomes]
rs9972498	0.88[CHB][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1523	chr15:45749900-45783825	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2433600	TMEM62	cis	cerebellum	SCAN
rs2433600	MGA	cis	parietal	SCAN
rs2433600	RPAP1	cis	cerebellum	SCAN
rs2433600	FAM82A2	cis	cerebellum	SCAN
rs2433600	SLC30A4	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45750800-45781000	Weak transcription	Stomach Mucosa	stomach
2	chr15:45751200-45801600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:45754200-45801600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:45757000-45794600	Weak transcription	Colonic Mucosa	Colon
5	chr15:45757000-45801800	Weak transcription	Gastric	stomach
6	chr15:45763400-45777200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr15:45767200-45813600	Weak transcription	Psoas Muscle	Psoas
8	chr15:45767400-45781000	Weak transcription	Lung	lung
9	chr15:45768200-45780200	Weak transcription	Fetal Stomach	stomach
10	chr15:45769200-45781400	Weak transcription	Osteobl	bone
11	chr15:45769200-45812000	Weak transcription	Small Intestine	intestine
12	chr15:45769400-45778000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:45769400-45791800	Weak transcription	NH-A	brain
14	chr15:45769400-45794600	Weak transcription	Fetal Intestine Small	intestine
15	chr15:45769400-45794800	Weak transcription	Ovary	ovary
16	chr15:45769400-45813000	Weak transcription	Fetal Intestine Large	intestine
17	chr15:45769600-45779200	Weak transcription	Liver	Liver
18	chr15:45769600-45780000	Weak transcription	Left Ventricle	heart
19	chr15:45769800-45778400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:45769800-45794600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:45770200-45780000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr15:45770200-45781000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:45770800-45779600	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:45771000-45778000	Weak transcription	Aorta	Aorta
25	chr15:45771000-45813400	Weak transcription	Right Ventricle	heart
26	chr15:45771200-45777200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:45771200-45814000	Weak transcription	Placenta	Placenta
28	chr15:45771400-45780200	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:45771600-45777000	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:45771800-45778400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:45772000-45779400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:45772000-45801600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:45772200-45779200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:45772200-45791000	Weak transcription	HSMM	muscle
35	chr15:45773200-45777200	Weak transcription	Primary B cells from cord blood	blood
36	chr15:45773200-45814000	Weak transcription	Pancreas	Pancrea
37	chr15:45773400-45777000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:45773400-45779400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:45773400-45790600	Weak transcription	HSMMtube	muscle
40	chr15:45773600-45779400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr15:45774000-45777000	Weak transcription	Adipose Nuclei	Adipose
42	chr15:45774200-45777000	Weak transcription	Brain Anterior Caudate	brain
43	chr15:45774600-45812800	Weak transcription	Fetal Brain Male	brain
44	chr15:45775000-45777600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr15:45775400-45786600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:45775600-45777600	Strong transcription	Primary T cells from cord blood	blood
47	chr15:45775600-45781600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:45775600-45791800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:45775600-45812800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr15:45775800-45780200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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