Variant report

Variant	rs1153830
Chromosome Location	chr15:45773124-45773125
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 57 )
Associated
traits (count: 0)

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];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1153831	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];0.91[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];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[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]
rs1768458	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2088164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2433600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2433617	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2433619	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486287	0.88[CHB][hapmap]
rs35828336	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4448883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs56179992	0.83[EUR][1000 genomes]
rs56405528	0.84[EUR][1000 genomes]
rs59574269	0.90[AMR][1000 genomes]
rs60350201	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60992352	0.83[EUR][1000 genomes]
rs61193305	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493154	0.82[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6493160	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7165838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7169748	1.00[CEU][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7170090	1.00[CEU][hapmap]
rs7171406	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7173983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72711264	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711278	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711279	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711280	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711283	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711284	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72711290	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72711294	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72711301	0.83[EUR][1000 genomes]
rs72713103	0.83[EUR][1000 genomes]
rs72713104	0.82[EUR][1000 genomes]
rs72713105	0.82[EUR][1000 genomes]
rs8023437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8025407	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8029509	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040466	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8042811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9972498	0.88[CHB][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

No data

Chromatin state (count:52 , 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	chr15:45762000-45773800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:45763400-45777200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr15:45767200-45813600	Weak transcription	Psoas Muscle	Psoas
9	chr15:45767400-45781000	Weak transcription	Lung	lung
10	chr15:45767600-45775600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:45767600-45775600	Weak transcription	Esophagus	oesophagus
12	chr15:45768200-45780200	Weak transcription	Fetal Stomach	stomach
13	chr15:45768800-45776000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr15:45769200-45781400	Weak transcription	Osteobl	bone
15	chr15:45769200-45812000	Weak transcription	Small Intestine	intestine
16	chr15:45769400-45775600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:45769400-45778000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:45769400-45791800	Weak transcription	NH-A	brain
19	chr15:45769400-45794600	Weak transcription	Fetal Intestine Small	intestine
20	chr15:45769400-45794800	Weak transcription	Ovary	ovary
21	chr15:45769400-45813000	Weak transcription	Fetal Intestine Large	intestine
22	chr15:45769600-45779200	Weak transcription	Liver	Liver
23	chr15:45769600-45780000	Weak transcription	Left Ventricle	heart
24	chr15:45769800-45778400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:45769800-45794600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:45770200-45780000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr15:45770200-45781000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:45770800-45779600	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:45771000-45775600	Weak transcription	Primary T cells from cord blood	blood
30	chr15:45771000-45778000	Weak transcription	Aorta	Aorta
31	chr15:45771000-45813400	Weak transcription	Right Ventricle	heart
32	chr15:45771200-45777200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:45771200-45814000	Weak transcription	Placenta	Placenta
34	chr15:45771400-45780200	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:45771600-45777000	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:45771800-45778400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:45772000-45779400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:45772000-45801600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:45772200-45779200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:45772200-45791000	Weak transcription	HSMM	muscle
41	chr15:45772600-45773200	Strong transcription	Primary B cells from cord blood	blood
42	chr15:45772600-45773800	Strong transcription	Brain Anterior Caudate	brain
43	chr15:45772600-45774000	Strong transcription	Adipose Nuclei	Adipose
44	chr15:45772800-45773400	Strong transcription	HSMMtube	muscle
45	chr15:45772800-45774000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
46	chr15:45773000-45773400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
47	chr15:45773000-45773400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr15:45773000-45773800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
49	chr15:45773000-45773800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:45773000-45774000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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