Variant report

Variant	rs6546753
Chromosome Location	chr2:72490319-72490320
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 132 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1000523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1003672	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10173381	0.90[ASW][hapmap];0.86[AFR][1000 genomes]
rs10175915	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs10178138	1.00[CHB][hapmap];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[CEU][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10193543	0.85[ASN][1000 genomes]
rs10196589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10204415	0.83[GIH][hapmap]
rs10205108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs10207299	0.92[AFR][1000 genomes]
rs10209861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10221769	1.00[CHB][hapmap];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[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1159763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1159764	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs1159765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1159766	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs12151496	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12466026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12466112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13382986	0.85[ASN][1000 genomes]
rs13387630	0.85[ASN][1000 genomes]
rs13389524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13391463	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392314	0.85[ASN][1000 genomes]
rs13395204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404369	0.93[ASN][1000 genomes]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13417114	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13418637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13423761	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13430651	0.85[ASN][1000 genomes]
rs13432350	0.90[ASW][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.96[AFR][1000 genomes]
rs17673916	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17724205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17724860	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17725024	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1860852	0.80[ASN][1000 genomes]
rs194235	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.87[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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2109963	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]
rs2159823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2192014	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2192015	0.92[GIH][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28278	0.86[ASN][1000 genomes]
rs3115351	0.81[ASW][hapmap]
rs34837782	0.80[ASN][1000 genomes]
rs41386	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41387	1.00[CHB][hapmap]
rs41388	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41389	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41390	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs41391	0.86[ASN][1000 genomes]
rs41392	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs41393	1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41394	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41395	0.93[ASN][1000 genomes]
rs41396	1.00[CHB][hapmap];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]
rs41399	1.00[CHB][hapmap]
rs41400	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs41401	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs41402	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs41403	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41405	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs41406	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs41407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs41408	1.00[CHB][hapmap];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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852288	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs4852859	0.85[ASN][1000 genomes]
rs4852860	0.93[ASN][1000 genomes]
rs4852861	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852862	0.93[ASN][1000 genomes]
rs55764675	0.85[ASN][1000 genomes]
rs55877105	0.87[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	0.88[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]
rs641939	0.81[ASW][hapmap]
rs642652	0.81[ASW][hapmap]
rs6546750	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6546755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546756	1.00[AFR][1000 genomes]
rs6546759	0.86[AFR][1000 genomes]
rs663218	0.90[ASW][hapmap]
rs666233	0.81[ASW][hapmap]
rs6719255	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6748607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760895	1.00[CEU][hapmap];1.00[CHB][hapmap];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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559131	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs7565922	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583271	0.87[GIH][hapmap]
rs7595180	0.82[AFR][1000 genomes]
rs768042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768043	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9309464	0.90[ASW][hapmap];0.80[AFR][1000 genomes]
rs9679148	0.92[AMR][1000 genomes];0.96[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6546753	MPHOSPH10	cis	cerebellum	SCAN
rs6546753	PCYOX1	cis	cerebellum	SCAN
rs6546753	MOGS	cis	cerebellum	SCAN
rs6546753	TPRKB	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72465800-72490400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:72485200-72501800	Weak transcription	HSMMtube	muscle
3	chr2:72488200-72496600	Weak transcription	Psoas Muscle	Psoas
4	chr2:72489200-72508200	Weak transcription	Aorta	Aorta
5	chr2:72489800-72491400	Enhancers	Brain Substantia Nigra	brain
6	chr2:72490000-72491200	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr2:72490000-72491200	Enhancers	A549	lung
8	chr2:72490000-72491400	Enhancers	Fetal Heart	heart
9	chr2:72490200-72490400	Enhancers	Pancreas	Pancrea
10	chr2:72490200-72490600	Enhancers	Fetal Muscle Leg	muscle
11	chr2:72490200-72490600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr2:72490200-72490600	Enhancers	Small Intestine	intestine
13	chr2:72490200-72490800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:72490200-72491000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:72490200-72491000	Enhancers	NH-A	brain
16	chr2:72490200-72491200	Enhancers	Brain Anterior Caudate	brain
17	chr2:72490200-72491200	Enhancers	Brain Hippocampus Middle	brain
18	chr2:72490200-72491200	Enhancers	Colonic Mucosa	Colon
19	chr2:72490200-72491200	Enhancers	Left Ventricle	heart
20	chr2:72490200-72491200	Enhancers	Ovary	ovary
21	chr2:72490200-72491200	Enhancers	Osteobl	bone
22	chr2:72490200-72491400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:72490200-72491400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:72490200-72491400	Enhancers	Brain Angular Gyrus	brain
25	chr2:72490200-72491400	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:72490200-72491400	Enhancers	Rectal Mucosa Donor 31	rectum

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