Variant report

Variant	rs2109963
Chromosome Location	chr2:72499725-72499726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1000523	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1003672	0.93[ASN][1000 genomes]
rs10173381	0.82[MKK][hapmap]
rs10175915	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs10178138	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10178847	0.85[ASN][1000 genomes]
rs10181899	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10190799	0.93[ASN][1000 genomes]
rs10192800	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10193543	0.85[ASN][1000 genomes]
rs10196589	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10204415	0.83[GIH][hapmap]
rs10205108	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10209861	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221767	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10221769	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11126362	0.86[ASN][1000 genomes]
rs11126363	0.93[ASN][1000 genomes]
rs1123199	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1159763	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1159764	0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1159765	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1159766	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11675268	1.00[JPT][hapmap]
rs12151496	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12466026	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12466112	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13382986	0.85[ASN][1000 genomes]
rs13387630	0.85[ASN][1000 genomes]
rs13389524	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13391463	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392314	0.85[ASN][1000 genomes]
rs13395204	1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404369	0.93[ASN][1000 genomes]
rs13416674	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13417114	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13418637	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13423761	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430254	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13430651	0.85[ASN][1000 genomes]
rs13432350	0.87[GIH][hapmap];0.84[MKK][hapmap]
rs17008208	1.00[JPT][hapmap]
rs17673916	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17724205	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17724860	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17725024	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1860852	0.80[ASN][1000 genomes]
rs194235	1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs194239	0.82[ASN][1000 genomes]
rs194242	0.86[ASN][1000 genomes]
rs194243	0.86[ASN][1000 genomes]
rs2041563	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041564	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080044	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2159823	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2192014	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2192015	0.92[GIH][hapmap];0.85[MKK][hapmap];0.80[AMR][1000 genomes]
rs28278	0.86[ASN][1000 genomes]
rs34837782	0.80[ASN][1000 genomes]
rs41386	1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41388	1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41389	1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41390	0.86[ASN][1000 genomes]
rs41391	0.86[ASN][1000 genomes]
rs41392	0.93[ASN][1000 genomes]
rs41393	1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41394	1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41395	0.93[ASN][1000 genomes]
rs41396	0.86[ASN][1000 genomes]
rs41397	0.80[ASN][1000 genomes]
rs41398	1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[ASN][1000 genomes]
rs41400	0.86[ASN][1000 genomes]
rs41401	1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs41402	1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs41403	1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41405	0.86[ASN][1000 genomes]
rs41406	0.93[ASN][1000 genomes]
rs41407	1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41408	1.00[JPT][hapmap]
rs41410	0.87[ASN][1000 genomes]
rs41411	0.87[ASN][1000 genomes]
rs41412	0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs41413	0.91[GIH][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs41414	0.80[ASN][1000 genomes]
rs41415	0.83[GIH][hapmap]
rs41416	0.83[GIH][hapmap]
rs41417	0.87[GIH][hapmap]
rs41418	0.80[ASN][1000 genomes]
rs41419	0.80[ASN][1000 genomes]
rs4852285	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852288	0.87[GIH][hapmap]
rs4852859	0.85[ASN][1000 genomes]
rs4852860	0.93[ASN][1000 genomes]
rs4852861	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852862	0.93[ASN][1000 genomes]
rs55764675	0.85[ASN][1000 genomes]
rs55877105	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55970539	0.85[ASN][1000 genomes]
rs56299443	0.85[ASN][1000 genomes]
rs62147573	0.85[ASN][1000 genomes]
rs62147579	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147589	0.85[ASN][1000 genomes]
rs62147626	0.85[ASN][1000 genomes]
rs62147629	0.85[ASN][1000 genomes]
rs62147636	0.85[ASN][1000 genomes]
rs6546750	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546752	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6546753	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546755	1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546756	0.80[AFR][1000 genomes]
rs6719255	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6748607	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751276	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760895	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559131	0.87[GIH][hapmap]
rs7565922	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583271	0.87[GIH][hapmap]
rs768042	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768043	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309463	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9679148	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72485200-72501800	Weak transcription	HSMMtube	muscle
2	chr2:72489200-72508200	Weak transcription	Aorta	Aorta
3	chr2:72491200-72502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:72496400-72500000	Enhancers	Fetal Heart	heart
5	chr2:72497200-72503400	Enhancers	Fetal Intestine Large	intestine
6	chr2:72497400-72500600	Weak transcription	Pancreas	Pancrea
7	chr2:72497400-72505400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:72498000-72499800	Enhancers	Brain Anterior Caudate	brain
9	chr2:72498000-72500000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:72498000-72503000	Enhancers	Fetal Intestine Small	intestine
11	chr2:72498200-72499800	Enhancers	Brain Hippocampus Middle	brain
12	chr2:72498200-72500200	Enhancers	Fetal Kidney	kidney
13	chr2:72498200-72501600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr2:72498200-72502400	Flanking Active TSS	A549	lung
15	chr2:72498400-72499800	Enhancers	Fetal Lung	lung
16	chr2:72498400-72501000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:72498400-72502800	Enhancers	Duodenum Mucosa	Duodenum
18	chr2:72498600-72499800	Enhancers	Brain Substantia Nigra	brain
19	chr2:72498600-72499800	Enhancers	Ovary	ovary
20	chr2:72498600-72499800	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr2:72498800-72499800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:72498800-72499800	Enhancers	Liver	Liver
23	chr2:72498800-72499800	Enhancers	Fetal Stomach	stomach
24	chr2:72499000-72499800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:72499000-72502400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:72499200-72499800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:72499200-72499800	Enhancers	Fetal Brain Male	brain
28	chr2:72499200-72499800	Enhancers	Stomach Mucosa	stomach
29	chr2:72499200-72499800	Enhancers	NHEK	skin
30	chr2:72499400-72500600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:72499400-72500600	Weak transcription	Hela-S3	cervix
32	chr2:72499400-72502200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:72499400-72503000	Weak transcription	Left Ventricle	heart
34	chr2:72499400-72507800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:72499400-72507800	Weak transcription	Psoas Muscle	Psoas
36	chr2:72499600-72501400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:72499600-72501600	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:72499600-72501800	Weak transcription	Brain Germinal Matrix	brain
39	chr2:72499600-72501800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:72499600-72502200	Weak transcription	Small Intestine	intestine
41	chr2:72499600-72502800	Weak transcription	Right Atrium	heart
42	chr2:72499600-72510400	Weak transcription	Right Ventricle	heart

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