Variant report

Variant	rs1153829
Chromosome Location	chr15:45777344-45777345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10851425	0.93[JPT][hapmap]
rs1153830	0.93[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1153831	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]
rs1153832	0.93[JPT][hapmap]
rs1288863	0.93[JPT][hapmap]
rs1288865	0.93[JPT][hapmap]
rs16944629	0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs16952731	0.93[JPT][hapmap]
rs1768458	0.88[AFR][1000 genomes]
rs2088164	0.93[JPT][hapmap]
rs2433600	0.93[JPT][hapmap]
rs2433617	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2433619	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4448883	0.93[JPT][hapmap]
rs60350201	0.85[AFR][1000 genomes]
rs6493154	0.94[ASW][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6493157	0.87[ASW][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs6493158	0.93[JPT][hapmap]
rs7165838	0.93[JPT][hapmap];0.82[YRI][hapmap]
rs7169748	0.86[YRI][hapmap]
rs7173983	0.93[JPT][hapmap];0.86[YRI][hapmap]
rs8023437	0.88[ASW][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap]
rs8029509	0.94[AFR][1000 genomes]
rs8040466	0.93[AFR][1000 genomes]
rs8042811	0.93[JPT][hapmap];0.85[LWK][hapmap]
rs8043334	0.83[YRI][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	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
5	nsv519435	chr15:45777344-45779008	Strong transcription Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1153829	SPATA5L1	cis	cerebellum	SCAN
rs1153829	TP53BP1	cis	parietal	SCAN
rs1153829	SLC30A4	cis	parietal	SCAN
rs1153829	RPAP1	cis	cerebellum	SCAN

Chromatin state (count:59 , 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	chr15:45767200-45813600	Weak transcription	Psoas Muscle	Psoas
7	chr15:45767400-45781000	Weak transcription	Lung	lung
8	chr15:45768200-45780200	Weak transcription	Fetal Stomach	stomach
9	chr15:45769200-45781400	Weak transcription	Osteobl	bone
10	chr15:45769200-45812000	Weak transcription	Small Intestine	intestine
11	chr15:45769400-45778000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:45769400-45791800	Weak transcription	NH-A	brain
13	chr15:45769400-45794600	Weak transcription	Fetal Intestine Small	intestine
14	chr15:45769400-45794800	Weak transcription	Ovary	ovary
15	chr15:45769400-45813000	Weak transcription	Fetal Intestine Large	intestine
16	chr15:45769600-45779200	Weak transcription	Liver	Liver
17	chr15:45769600-45780000	Weak transcription	Left Ventricle	heart
18	chr15:45769800-45778400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:45769800-45794600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:45770200-45780000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:45770200-45781000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:45770800-45779600	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:45771000-45778000	Weak transcription	Aorta	Aorta
24	chr15:45771000-45813400	Weak transcription	Right Ventricle	heart
25	chr15:45771200-45814000	Weak transcription	Placenta	Placenta
26	chr15:45771400-45780200	Weak transcription	Fetal Muscle Leg	muscle
27	chr15:45771800-45778400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:45772000-45779400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:45772000-45801600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:45772200-45779200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:45772200-45791000	Weak transcription	HSMM	muscle
32	chr15:45773200-45814000	Weak transcription	Pancreas	Pancrea
33	chr15:45773400-45779400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:45773400-45790600	Weak transcription	HSMMtube	muscle
35	chr15:45773600-45779400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:45774600-45812800	Weak transcription	Fetal Brain Male	brain
37	chr15:45775000-45777600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr15:45775400-45786600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:45775600-45777600	Strong transcription	Primary T cells from cord blood	blood
40	chr15:45775600-45781600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:45775600-45791800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:45775600-45812800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr15:45775800-45780200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:45776000-45800400	Weak transcription	Esophagus	oesophagus
45	chr15:45776600-45780800	Weak transcription	NHDF-Ad	bronchial
46	chr15:45776600-45783600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:45776800-45781800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:45777000-45777600	Genic enhancers	Brain Hippocampus Middle	brain
49	chr15:45777000-45777600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr15:45777000-45777600	Enhancers	Brain Substantia Nigra	brain

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