Variant report

Variant	rs17108107
Chromosome Location	chr14:70877771-70877772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10131943	0.91[JPT][hapmap]
rs10133282	0.80[EUR][1000 genomes]
rs10139500	0.83[EUR][1000 genomes]
rs10144818	0.84[EUR][1000 genomes]
rs10150707	0.80[EUR][1000 genomes]
rs10483830	0.87[CEU][hapmap]
rs11625168	0.87[JPT][hapmap]
rs11844845	0.80[EUR][1000 genomes]
rs12436464	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12436902	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12586325	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs12586328	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs12586722	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108246	0.87[CEU][hapmap]
rs17108264	0.87[CEU][hapmap]
rs17108274	0.87[CEU][hapmap]
rs17113651	0.87[CEU][hapmap]
rs1953798	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs1959483	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap]
rs2877657	0.80[EUR][1000 genomes]
rs3751523	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764182	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4143920	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs4902817	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58186506	0.84[EUR][1000 genomes]
rs7141636	0.84[EUR][1000 genomes]
rs7150428	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7159587	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7161249	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72735756	0.94[ASN][1000 genomes]
rs73291972	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8008210	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8012142	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8014179	0.84[EUR][1000 genomes]
rs8014252	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8014338	0.87[ASN][1000 genomes]
rs8015163	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8020009	0.94[EUR][1000 genomes];0.95[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	nsv902075	chr14:70612618-70919016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17108107	MED6	cis	cerebellum	SCAN
rs17108107	ZFYVE1	cis	parietal	SCAN
rs17108107	SLC8A3	cis	cerebellum	SCAN
rs17108107	PLEKHH1	cis	parietal	SCAN
rs17108107	MED6	cis	parietal	SCAN
rs17108107	ADAM20	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70827200-70882600	Weak transcription	A549	lung
2	chr14:70827200-70882600	Weak transcription	NH-A	brain
3	chr14:70833800-70882400	Weak transcription	NHDF-Ad	bronchial
4	chr14:70838600-70882400	Weak transcription	Hela-S3	cervix
5	chr14:70840200-70882400	Weak transcription	Colon Smooth Muscle	Colon
6	chr14:70840200-70882600	Weak transcription	Colonic Mucosa	Colon
7	chr14:70840800-70882800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:70841000-70882600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr14:70841400-70879800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr14:70842600-70882400	Weak transcription	Fetal Kidney	kidney
11	chr14:70846800-70878600	Weak transcription	HSMM	muscle
12	chr14:70848400-70882400	Weak transcription	Brain Angular Gyrus	brain
13	chr14:70848400-70882800	Weak transcription	Psoas Muscle	Psoas
14	chr14:70848400-70883000	Weak transcription	HSMMtube	muscle
15	chr14:70848600-70882400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr14:70848600-70882800	Weak transcription	Fetal Muscle Leg	muscle
17	chr14:70848800-70882600	Weak transcription	Brain Substantia Nigra	brain
18	chr14:70853600-70882400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:70853800-70880800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr14:70854800-70882400	Weak transcription	Brain Anterior Caudate	brain
21	chr14:70855200-70882400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr14:70856000-70882400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr14:70859000-70882800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr14:70864600-70880000	Weak transcription	Esophagus	oesophagus
25	chr14:70865000-70878400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr14:70865000-70882400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr14:70865000-70882800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr14:70865200-70882800	Weak transcription	Aorta	Aorta
29	chr14:70865400-70882600	Weak transcription	Brain Hippocampus Middle	brain
30	chr14:70865600-70880200	Weak transcription	HepG2	liver
31	chr14:70865800-70882600	Weak transcription	Adipose Nuclei	Adipose
32	chr14:70866000-70882600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr14:70866200-70878200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr14:70866400-70881600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:70866400-70882200	Weak transcription	Fetal Brain Female	brain
36	chr14:70866400-70882400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr14:70866400-70883000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr14:70866400-70883000	Weak transcription	Fetal Thymus	thymus
39	chr14:70866400-70883000	Weak transcription	Thymus	Thymus
40	chr14:70866400-70883000	Weak transcription	Spleen	Spleen
41	chr14:70866400-70883200	Weak transcription	Gastric	stomach
42	chr14:70866600-70878200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr14:70866600-70882600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr14:70866600-70882600	Weak transcription	Brain Germinal Matrix	brain
45	chr14:70866600-70882800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr14:70866600-70883000	Weak transcription	Lung	lung
47	chr14:70866800-70878400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr14:70866800-70878600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr14:70866800-70882400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr14:70866800-70882400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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