Variant report

Variant	rs2433617
Chromosome Location	chr15:45768909-45768910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10152697	0.86[CHB][hapmap]
rs10851425	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1153829	0.94[ASW][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1153830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153831	0.89[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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[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	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2088164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2433600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2433619	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2486287	0.88[CHB][hapmap]
rs35828336	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4448883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs56405528	0.82[ASN][1000 genomes]
rs60350201	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61193305	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493154	0.89[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493157	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6493158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6493160	0.81[AMR][1000 genomes]
rs7165838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7169748	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs7170090	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs7171406	0.81[AMR][1000 genomes]
rs7173983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72711264	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72711278	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72711279	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72711280	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72711283	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72711284	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711290	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711294	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8023437	0.84[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];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8025407	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap]
rs8029509	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8040466	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8042811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9972498	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	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
3	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2433617	GPR176	cis	cerebellum	SCAN
rs2433617	MGA	cis	parietal	SCAN
rs2433617	TMEM62	cis	cerebellum	SCAN
rs2433617	SLC30A4	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

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	chr15:45760800-45772800	Weak transcription	HSMMtube	muscle
7	chr15:45762000-45773800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:45763400-45777200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr15:45767200-45813600	Weak transcription	Psoas Muscle	Psoas
10	chr15:45767400-45781000	Weak transcription	Lung	lung
11	chr15:45767600-45775600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:45767600-45775600	Weak transcription	Esophagus	oesophagus
13	chr15:45768200-45769400	Enhancers	Fetal Intestine Large	intestine
14	chr15:45768200-45780200	Weak transcription	Fetal Stomach	stomach
15	chr15:45768400-45769400	Enhancers	Fetal Intestine Small	intestine
16	chr15:45768600-45769200	Enhancers	HepG2	liver
17	chr15:45768600-45773000	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr15:45768800-45769000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:45768800-45769200	Enhancers	Osteobl	bone
20	chr15:45768800-45769400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:45768800-45769400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:45768800-45769400	Enhancers	NH-A	brain
23	chr15:45768800-45776000	Strong transcription	Rectal Mucosa Donor 29	rectum

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