Variant report

Variant	rs1153831
Chromosome Location	chr15:45772448-45772449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45770928..45772641-chr15:45779670..45781462,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GATM-5	chr15:45771811-45773663	NONHSAT042257

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

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	0.94[ASW][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1153830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[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	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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];0.92[EUR][1000 genomes];0.85[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];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2433617	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2433619	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486287	0.88[CHB][hapmap]
rs35828336	0.90[EUR][1000 genomes];0.85[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];0.83[EUR][1000 genomes]
rs56179992	0.82[EUR][1000 genomes]
rs56405528	0.83[EUR][1000 genomes]
rs59574269	0.83[AMR][1000 genomes]
rs60350201	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60992352	0.82[EUR][1000 genomes]
rs61193305	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493154	1.00[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493157	0.94[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];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[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];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6493160	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7165838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7169748	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7170090	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs7171406	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7173983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72711264	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711278	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711279	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711280	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711283	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711284	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72711290	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72711294	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72711301	0.82[EUR][1000 genomes]
rs72713103	0.82[EUR][1000 genomes]
rs72713104	0.80[EUR][1000 genomes]
rs72713105	0.80[EUR][1000 genomes]
rs8023437	0.94[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];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8025407	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs8029509	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040466	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8043334	0.83[YRI][hapmap]
rs9972498	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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
rs1153831	SLC30A4	cis	parietal	SCAN
rs1153831	MGA	cis	parietal	SCAN
rs1153831	FAM82A2	cis	cerebellum	SCAN
rs1153831	RPAP1	cis	cerebellum	SCAN
rs1153831	TMEM62	cis	cerebellum	SCAN

Chromatin state (count:45 , 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	chr15:45768200-45780200	Weak transcription	Fetal Stomach	stomach
14	chr15:45768600-45773000	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr15:45768800-45776000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr15:45769200-45772600	Weak transcription	Adipose Nuclei	Adipose
17	chr15:45769200-45781400	Weak transcription	Osteobl	bone
18	chr15:45769200-45812000	Weak transcription	Small Intestine	intestine
19	chr15:45769400-45775600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:45769400-45778000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:45769400-45791800	Weak transcription	NH-A	brain
22	chr15:45769400-45794600	Weak transcription	Fetal Intestine Small	intestine
23	chr15:45769400-45794800	Weak transcription	Ovary	ovary
24	chr15:45769400-45813000	Weak transcription	Fetal Intestine Large	intestine
25	chr15:45769600-45772600	Weak transcription	Brain Anterior Caudate	brain
26	chr15:45769600-45779200	Weak transcription	Liver	Liver
27	chr15:45769600-45780000	Weak transcription	Left Ventricle	heart
28	chr15:45769800-45778400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:45769800-45794600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:45770200-45780000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:45770200-45781000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:45770800-45779600	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:45771000-45775600	Weak transcription	Primary T cells from cord blood	blood
34	chr15:45771000-45778000	Weak transcription	Aorta	Aorta
35	chr15:45771000-45813400	Weak transcription	Right Ventricle	heart
36	chr15:45771200-45777200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:45771200-45814000	Weak transcription	Placenta	Placenta
38	chr15:45771400-45780200	Weak transcription	Fetal Muscle Leg	muscle
39	chr15:45771600-45777000	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:45771800-45778400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:45772000-45779400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:45772000-45801600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:45772200-45779200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:45772200-45791000	Weak transcription	HSMM	muscle
45	chr15:45772400-45772600	ZNF genes & repeats	Primary B cells from cord blood	blood

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