Variant report

Variant	rs17108197
Chromosome Location	chr14:70982633-70982634
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 134 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1007402	0.85[CHB][hapmap];0.95[CHD][hapmap]
rs10129782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10130071	0.84[ASN][1000 genomes]
rs10131716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10133963	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10135356	0.83[ASN][1000 genomes]
rs10141744	0.80[ASN][1000 genomes]
rs10143254	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10144289	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs10144535	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10144653	0.85[ASN][1000 genomes]
rs10144696	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10147143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10150160	0.90[ASN][1000 genomes]
rs10483830	0.90[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs10483832	1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1057127	0.80[ASN][1000 genomes]
rs10873239	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1112478	0.82[ASN][1000 genomes]
rs11158863	0.86[ASN][1000 genomes]
rs11158867	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs1137491	0.81[ASN][1000 genomes]
rs12586441	0.86[ASN][1000 genomes]
rs12586886	0.84[ASN][1000 genomes]
rs12587666	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12587714	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12587866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12588723	0.86[ASN][1000 genomes]
rs12590117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12590198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12590217	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12590401	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12590471	0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12590610	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1538403	0.94[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108201	0.85[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];0.80[ASN][1000 genomes]
rs17108267	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17108274	0.90[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs17108276	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17108278	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17108280	1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17113651	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1953803	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1959477	0.82[ASN][1000 genomes]
rs1962311	0.85[CHB][hapmap]
rs1962312	0.81[ASN][1000 genomes]
rs2153114	0.90[CHB][hapmap]
rs2332431	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs28559756	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28612538	0.84[ASN][1000 genomes]
rs2877673	0.81[ASN][1000 genomes]
rs45523543	0.80[ASN][1000 genomes]
rs55965222	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56155089	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56322604	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56328037	0.81[ASN][1000 genomes]
rs56392092	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56687536	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56721095	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56922268	0.80[ASN][1000 genomes]
rs57032041	0.86[ASN][1000 genomes]
rs57339942	0.80[ASN][1000 genomes]
rs57598551	0.80[ASN][1000 genomes]
rs58069917	0.81[ASN][1000 genomes]
rs58092588	0.84[ASN][1000 genomes]
rs58258245	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58777530	0.86[ASN][1000 genomes]
rs58919501	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58985060	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59044667	0.81[ASN][1000 genomes]
rs59115232	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59233924	0.80[ASN][1000 genomes]
rs59475121	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59599422	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59748874	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60120955	0.80[ASN][1000 genomes]
rs60251828	0.80[ASN][1000 genomes]
rs60370428	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60453577	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60848570	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60860517	0.84[ASN][1000 genomes]
rs60862805	0.86[ASN][1000 genomes]
rs60867605	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60870618	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61388426	0.81[ASN][1000 genomes]
rs6420902	0.90[CHB][hapmap];0.98[CHD][hapmap]
rs6573972	0.85[ASN][1000 genomes]
rs6573973	0.82[ASN][1000 genomes]
rs66572616	0.80[ASN][1000 genomes]
rs7141056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7141562	0.82[ASN][1000 genomes]
rs7141713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7141730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7150354	0.92[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];1.00[ASN][1000 genomes]
rs7150545	0.82[ASN][1000 genomes]
rs7154858	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7154904	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7155436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7156661	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.93[ASN][1000 genomes]
rs7157073	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7157455	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7157618	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7157685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7158201	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7158848	0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[MEX][hapmap]
rs73282126	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73282127	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73282153	0.86[ASN][1000 genomes]
rs73283917	0.82[ASN][1000 genomes]
rs7359112	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs74062726	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs74062730	0.86[ASN][1000 genomes]
rs74062733	0.86[ASN][1000 genomes]
rs74062743	0.84[ASN][1000 genomes]
rs74062746	0.84[ASN][1000 genomes]
rs74062750	0.84[ASN][1000 genomes]
rs74062769	0.80[ASN][1000 genomes]
rs8004054	0.87[ASN][1000 genomes]
rs8005893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8006487	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8010044	0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[ASN][1000 genomes]
rs8010473	0.82[AMR][1000 genomes]
rs8011847	0.85[ASN][1000 genomes]
rs8012025	0.86[ASN][1000 genomes]
rs8016953	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8018765	0.82[ASN][1000 genomes]
rs8021911	0.82[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9323542	0.90[CHB][hapmap];0.80[ASN][1000 genomes]

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
rs17108197	MED6	cis	cerebellum	SCAN
rs17108197	SLC8A3	cis	cerebellum	SCAN
rs17108197	MED6	cis	parietal	SCAN
rs17108197	ADAM20	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70958600-70989000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr14:70958800-70993800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr14:70968600-70989400	Weak transcription	Pancreas	Pancrea
4	chr14:70973400-70985200	Weak transcription	Left Ventricle	heart
5	chr14:70975800-70990000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:70978200-70986600	Weak transcription	Liver	Liver
7	chr14:70978600-70985000	Weak transcription	Aorta	Aorta
8	chr14:70978800-70983000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:70978800-70988600	Weak transcription	Ovary	ovary
10	chr14:70979200-70986800	Weak transcription	Primary T cells from cord blood	blood
11	chr14:70980000-70989400	Weak transcription	Brain Angular Gyrus	brain
12	chr14:70980400-70982800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr14:70980400-70983200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr14:70981000-70989400	Weak transcription	Brain Substantia Nigra	brain
15	chr14:70981000-70989600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr14:70981200-70994400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr14:70981800-70984800	Weak transcription	HSMMtube	muscle
18	chr14:70982000-70982800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr14:70982000-71003600	Weak transcription	HSMM	muscle
20	chr14:70982400-71003200	Weak transcription	Psoas Muscle	Psoas
21	chr14:70982600-70985000	Weak transcription	Primary hematopoietic stem cells	blood

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