Variant report

Variant	rs10873239
Chromosome Location	chr14:71011734-71011735
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1007402	0.85[CHB][hapmap];0.95[CHD][hapmap]
rs10129782	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10130071	0.83[ASN][1000 genomes]
rs10131716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10133963	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10135356	0.81[ASN][1000 genomes]
rs10143254	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10144289	0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs10144535	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10144653	0.84[ASN][1000 genomes]
rs10144696	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10147143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10150160	0.89[ASN][1000 genomes]
rs10483830	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10483832	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1112478	0.80[ASN][1000 genomes]
rs11158863	0.85[ASN][1000 genomes]
rs11158867	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs12586441	0.85[ASN][1000 genomes]
rs12586886	0.83[ASN][1000 genomes]
rs12587666	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12587714	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12587866	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12588723	0.85[ASN][1000 genomes]
rs12590117	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12590198	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12590217	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12590401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590471	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12590610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1538403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17108197	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108201	0.84[ASN][1000 genomes]
rs17108246	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs17108264	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs17108267	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17108274	0.90[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs17108276	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17108278	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17108280	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17113651	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1953803	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1959477	0.80[ASN][1000 genomes]
rs1962311	0.85[CHB][hapmap]
rs2153114	0.90[CHB][hapmap]
rs2332431	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs28559756	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28612538	0.82[ASN][1000 genomes]
rs4143920	0.85[CEU][hapmap]
rs55965222	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56155089	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56322604	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56392092	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56687536	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56721095	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57032041	0.85[ASN][1000 genomes]
rs58092588	0.82[ASN][1000 genomes]
rs58258245	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58777530	0.84[ASN][1000 genomes]
rs58919501	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58985060	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59115232	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59475121	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59599422	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59748874	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60370428	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60453577	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60848570	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60860517	0.82[ASN][1000 genomes]
rs60862805	0.85[ASN][1000 genomes]
rs60867605	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60870618	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6420902	0.90[CHB][hapmap];0.98[CHD][hapmap]
rs6573972	0.84[ASN][1000 genomes]
rs6573973	0.81[ASN][1000 genomes]
rs7141056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7141562	0.81[ASN][1000 genomes]
rs7141713	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7141730	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7150354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7150545	0.81[ASN][1000 genomes]
rs7154858	0.86[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7154904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7155088	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7155436	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7156661	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs7157073	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7157455	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7157618	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7157685	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7158201	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7158848	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[MEX][hapmap]
rs73282126	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73282127	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73282153	0.84[ASN][1000 genomes]
rs73283917	0.81[ASN][1000 genomes]
rs7359112	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs74062726	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs74062730	0.85[ASN][1000 genomes]
rs74062733	0.85[ASN][1000 genomes]
rs74062743	0.82[ASN][1000 genomes]
rs74062746	0.82[ASN][1000 genomes]
rs74062750	0.82[ASN][1000 genomes]
rs8004054	0.86[ASN][1000 genomes]
rs8005893	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8006487	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8010044	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap]
rs8010473	0.82[AMR][1000 genomes]
rs8011847	0.84[ASN][1000 genomes]
rs8012025	0.85[ASN][1000 genomes]
rs8016953	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8018765	0.81[ASN][1000 genomes]
rs8021911	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9323542	0.85[CEU][hapmap];0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv565042	chr14:70951234-71011734	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1050615	chr14:70954149-71013235	Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2763072	chr14:70954149-71013247	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10873239	MED6	cis	cerebellum	SCAN
rs10873239	SLC8A3	cis	cerebellum	SCAN
rs10873239	MED6	cis	parietal	SCAN
rs10873239	ADAM20	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70988000-71028200	Weak transcription	Esophagus	oesophagus
2	chr14:70988000-71029800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr14:70988800-71028800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr14:70990400-71029600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr14:70991400-71028200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr14:70991600-71014600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr14:70991600-71022400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr14:70991600-71028200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr14:70991600-71028800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr14:70991800-71011800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:70992200-71022600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr14:70999800-71022400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:70999800-71024600	Weak transcription	Colon Smooth Muscle	Colon
14	chr14:70999800-71029200	Weak transcription	Brain Anterior Caudate	brain
15	chr14:70999800-71030200	Weak transcription	Brain Angular Gyrus	brain
16	chr14:71000000-71028800	Weak transcription	Primary T cells from cord blood	blood
17	chr14:71004000-71030200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr14:71004200-71022600	Weak transcription	Spleen	Spleen
19	chr14:71004200-71028000	Weak transcription	Primary B cells from cord blood	blood
20	chr14:71004200-71034600	Weak transcription	Brain Substantia Nigra	brain
21	chr14:71004400-71011800	Weak transcription	Aorta	Aorta
22	chr14:71004400-71011800	Weak transcription	Left Ventricle	heart
23	chr14:71004400-71012000	Weak transcription	Pancreas	Pancrea
24	chr14:71004400-71022400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr14:71004400-71028000	Weak transcription	Liver	Liver
26	chr14:71004400-71029800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr14:71004400-71030000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr14:71004600-71011800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr14:71004600-71011800	Weak transcription	Adipose Nuclei	Adipose
30	chr14:71005000-71012000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr14:71005000-71022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr14:71007000-71029200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr14:71010000-71014000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr14:71010400-71012200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr14:71010800-71029000	Weak transcription	Fetal Lung	lung
36	chr14:71011000-71014000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr14:71011400-71022400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr14:71011600-71012200	Strong transcription	Ovary	ovary

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