Variant report

Variant	rs17108201
Chromosome Location	chr14:70988931-70988932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70983745..70986575-chr14:70987708..70990108,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10129782	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10131716	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10135356	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10144289	0.81[CHB][hapmap]
rs10147143	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10483830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10483832	0.90[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs10873239	0.84[ASN][1000 genomes]
rs11158863	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158867	0.81[CHB][hapmap]
rs12586299	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12586325	0.87[CEU][hapmap]
rs12586328	0.87[CEU][hapmap]
rs12586392	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12586441	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12587666	0.80[ASN][1000 genomes]
rs12587714	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12587866	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12588723	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12590117	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12590198	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12590217	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12590401	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12590471	0.81[CHB][hapmap]
rs12590610	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1538403	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17108107	0.87[CEU][hapmap]
rs17108197	0.85[ASN][1000 genomes]
rs17108246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17108264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17108274	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17108280	0.90[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs17113651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1953798	0.87[CEU][hapmap]
rs1953803	0.84[ASN][1000 genomes]
rs1959477	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1959483	0.87[CEU][hapmap]
rs2153114	0.81[CHB][hapmap]
rs2332431	0.90[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs2332432	0.88[ASN][1000 genomes]
rs28559756	0.85[ASN][1000 genomes]
rs28612538	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2877672	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45523543	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902817	0.87[CEU][hapmap]
rs56071949	0.88[AFR][1000 genomes]
rs56328037	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56392092	0.85[ASN][1000 genomes]
rs56721095	0.86[ASN][1000 genomes]
rs56922268	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57032041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57339942	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57598551	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58069917	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58092588	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58777530	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59044667	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59233924	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60120955	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60251828	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60555424	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60848570	0.81[ASN][1000 genomes]
rs60860517	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60862805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60867605	0.80[ASN][1000 genomes]
rs60870618	0.84[ASN][1000 genomes]
rs61388426	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6420902	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs66572616	0.89[ASN][1000 genomes]
rs7141056	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7141713	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7141730	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7145530	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7150354	0.89[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7154858	0.81[CHB][hapmap]
rs7154904	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7155088	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7155436	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7156661	0.90[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs7157618	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7157685	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7158201	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7158848	0.81[CHB][hapmap]
rs73282126	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73282127	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73282153	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73283917	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74062726	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74062730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74062733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74062743	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74062745	0.84[AFR][1000 genomes]
rs74062746	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74062750	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74062769	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8005893	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs8006487	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8010044	0.81[CHB][hapmap]
rs8010473	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8012025	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8014252	0.87[CEU][hapmap]
rs8016953	0.85[ASN][1000 genomes]
rs8021911	0.90[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs9323542	0.81[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17108201	MED6	cis	cerebellum	SCAN
rs17108201	MED6	cis	parietal	SCAN
rs17108201	ZFYVE1	cis	parietal	SCAN
rs17108201	UPF0639	cis	parietal	SCAN
rs17108201	ARFGEF2	trans	parietal	SCAN
rs17108201	ADAM20	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

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	chr14:70975800-70990000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:70980000-70989400	Weak transcription	Brain Angular Gyrus	brain
6	chr14:70981000-70989400	Weak transcription	Brain Substantia Nigra	brain
7	chr14:70981000-70989600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr14:70981200-70994400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr14:70982000-71003600	Weak transcription	HSMM	muscle
10	chr14:70982400-71003200	Weak transcription	Psoas Muscle	Psoas
11	chr14:70982800-70989400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr14:70983800-70989400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr14:70985800-70989400	Weak transcription	Left Ventricle	heart
14	chr14:70985800-71003800	Weak transcription	HSMMtube	muscle
15	chr14:70986000-70991800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr14:70987000-70989800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr14:70987200-70989400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr14:70987600-70990200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr14:70987600-70993200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr14:70987800-70989400	Weak transcription	Adipose Nuclei	Adipose
21	chr14:70987800-70989400	Weak transcription	Liver	Liver
22	chr14:70987800-70989400	Weak transcription	Brain Anterior Caudate	brain
23	chr14:70987800-70989400	Weak transcription	Gastric	stomach
24	chr14:70987800-70990800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr14:70987800-70995800	Weak transcription	Colon Smooth Muscle	Colon
26	chr14:70987800-71005800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr14:70988000-70989400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr14:70988000-70989400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr14:70988000-70989400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr14:70988000-70989600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr14:70988000-70989800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr14:70988000-70990600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr14:70988000-70991000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:70988000-70991000	Weak transcription	Brain Hippocampus Middle	brain
35	chr14:70988000-70991000	Weak transcription	Spleen	Spleen
36	chr14:70988000-71028200	Weak transcription	Esophagus	oesophagus
37	chr14:70988000-71029800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr14:70988200-70989600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr14:70988200-70989800	Weak transcription	Right Ventricle	heart
40	chr14:70988200-70990200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:70988200-70990800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:70988200-70991400	Strong transcription	Primary T cells from cord blood	blood
43	chr14:70988400-70994600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:70988400-71003800	Weak transcription	Primary B cells from cord blood	blood
45	chr14:70988600-70989400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr14:70988600-70989800	ZNF genes & repeats	Aorta	Aorta
47	chr14:70988600-70990200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr14:70988600-70991600	ZNF genes & repeats	Ovary	ovary
49	chr14:70988600-70993000	Weak transcription	Brain Germinal Matrix	brain
50	chr14:70988600-70993200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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