Variant report

Variant	rs1073540
Chromosome Location	chr9:72829814-72829815
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10114215	0.82[ASN][1000 genomes]
rs10491653	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10868808	0.91[CHB][hapmap]
rs11142363	0.91[CHB][hapmap]
rs11142367	0.92[CHB][hapmap]
rs11142368	0.92[CHB][hapmap]
rs11142370	0.92[CHB][hapmap]
rs11142373	0.92[CHB][hapmap]
rs1180101	0.92[CHB][hapmap]
rs1180102	0.92[CHB][hapmap]
rs1180104	0.92[CHB][hapmap]
rs1180105	0.92[CHB][hapmap]
rs1180107	0.92[CHB][hapmap]
rs1180112	0.91[CHB][hapmap]
rs1180117	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs1180118	0.92[CHB][hapmap]
rs1180122	0.92[CHB][hapmap]
rs1180124	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1180126	0.92[CHB][hapmap]
rs1180133	0.92[CHB][hapmap]
rs11998951	0.92[CHB][hapmap]
rs12006212	0.92[CHB][hapmap]
rs12156606	0.83[CHB][hapmap]
rs12380844	0.92[CHB][hapmap]
rs12683706	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12683986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12684301	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12684987	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12685322	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12685441	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12685491	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12685534	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12686312	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12686573	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12686584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12686850	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17051690	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17051696	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17052443	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17052748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17053503	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17088796	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17088840	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17088889	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17088905	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1927116	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1927117	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1927119	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1927142	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927143	0.87[ASN][1000 genomes]
rs1927148	0.92[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1927150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2026137	0.92[CHB][hapmap]
rs2026138	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2148853	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2148865	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2182732	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296772	0.87[AMR][1000 genomes]
rs2296773	0.87[AMR][1000 genomes]
rs2871290	0.84[ASN][1000 genomes]
rs2871293	0.92[CHB][hapmap]
rs2871295	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015223	0.87[AMR][1000 genomes]
rs34061327	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35188046	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35508139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3739773	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3739774	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4069793	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4287005	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4410968	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4439194	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4449855	0.92[CHB][hapmap]
rs4495496	0.87[AMR][1000 genomes]
rs4596711	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4602958	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4606121	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4610818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4621877	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744982	0.84[ASN][1000 genomes]
rs4744994	0.92[CHB][hapmap]
rs56735283	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56860643	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57048128	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57398306	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57477024	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58219953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58662316	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58948879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58969772	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58976318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59010963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59189596	0.84[ASN][1000 genomes]
rs59444215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59546243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59589460	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59619263	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59960592	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59976188	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60049462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60391643	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60458589	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61092050	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61265226	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61266539	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7022893	0.82[ASN][1000 genomes]
rs7034322	0.92[CHB][hapmap]
rs7046167	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs716535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753022	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753023	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7858988	0.92[CHB][hapmap]
rs7875348	0.84[ASN][1000 genomes]
rs943536	0.92[CHB][hapmap]
rs943540	0.92[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs954808	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72793000-72842600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72809600-72837800	Weak transcription	NH-A	brain
3	chr9:72820800-72835400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:72821200-72844800	Weak transcription	HMEC	breast
5	chr9:72821400-72830200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:72821400-72832000	Weak transcription	NHEK	skin
7	chr9:72825600-72833200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:72826000-72833200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:72827200-72830800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr9:72827200-72832000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:72827400-72830200	Weak transcription	Colonic Mucosa	Colon
12	chr9:72827600-72833800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:72827600-72834000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:72827600-72843200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:72827800-72833200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:72827800-72833400	Weak transcription	Osteobl	bone
17	chr9:72827800-72841600	Weak transcription	Placenta	Placenta
18	chr9:72828000-72830200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr9:72828000-72832000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:72828000-72833200	Weak transcription	Fetal Stomach	stomach
21	chr9:72828000-72833200	Weak transcription	Left Ventricle	heart
22	chr9:72828000-72833400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:72828000-72836600	Weak transcription	Right Ventricle	heart
24	chr9:72828000-72837000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:72828000-72844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:72828000-72858800	Weak transcription	Gastric	stomach
27	chr9:72828200-72831400	Strong transcription	HSMMtube	muscle
28	chr9:72828200-72831600	Strong transcription	Liver	Liver
29	chr9:72828200-72833200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:72828200-72833400	Weak transcription	Fetal Kidney	kidney
31	chr9:72828200-72835400	Weak transcription	Adipose Nuclei	Adipose
32	chr9:72828200-72835400	Weak transcription	Small Intestine	intestine
33	chr9:72828200-72843200	Weak transcription	Fetal Lung	lung
34	chr9:72828200-72844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:72828400-72830800	Weak transcription	Brain Hippocampus Middle	brain
36	chr9:72828400-72830800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr9:72828400-72831400	Weak transcription	HepG2	liver
38	chr9:72828400-72831600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr9:72828600-72830200	Strong transcription	Pancreas	Pancrea
40	chr9:72828600-72837200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:72828600-72843000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:72828800-72830800	Strong transcription	Ovary	ovary
43	chr9:72828800-72831000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:72828800-72831600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:72829000-72830200	ZNF genes & repeats	Fetal Muscle Leg	muscle
46	chr9:72829000-72831000	Weak transcription	Esophagus	oesophagus
47	chr9:72829000-72831600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:72829000-72841800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:72829200-72830200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:72829400-72830200	Weak transcription	HSMM	muscle

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