Variant report

Variant	rs8052125
Chromosome Location	chr16:70537329-70537330
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:70536505..70539456-chr16:70548133..70550767,2	MCF-7	breast:
2	chr16:70536864..70540404-chr16:70556076..70558403,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189091	Chromatin interaction
ENSG00000103051	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10852465	0.80[ASN][1000 genomes]
rs11075767	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075768	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075769	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11075770	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11640374	0.96[CEU][hapmap]
rs11641683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643344	0.88[ASN][1000 genomes]
rs11643373	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs11645214	0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11645287	0.96[CEU][hapmap]
rs11645437	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11645585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648402	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11649624	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11865527	0.88[ASN][1000 genomes]
rs11866400	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12447090	0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs12597401	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12909	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12925729	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12933634	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2168606	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2288491	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303791	0.89[ASW][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes]
rs2303792	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2303793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33910368	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34567847	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34890962	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3859068	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4277334	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4284632	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4324119	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4432264	0.82[AMR][1000 genomes]
rs4436771	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4513092	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4592653	0.96[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4985533	0.89[ASW][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs4985534	0.89[ASW][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs58963621	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6499317	0.90[AMR][1000 genomes]
rs6499320	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6499321	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71401814	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7189474	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7190039	1.00[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs7192268	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7194521	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7195030	0.81[ASN][1000 genomes]
rs7197262	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7197840	0.83[EUR][1000 genomes]
rs7198317	0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7199859	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7200430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201750	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7204583	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs722579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744672	0.85[ASN][1000 genomes]
rs7919	0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8045651	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046881	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8049641	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8049786	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8051506	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8052031	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8053436	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8057610	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8058224	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs8062178	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8062183	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs8063990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936994	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9635522	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9929904	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934440	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9936225	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv3330254	chr16:70536801-70538799	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv2047908	chr16:70537300-70537988	Strong transcription Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs8052125	RP11-296I10.6	cis	Thyroid	GTEx
rs8052125	EXOSC6	cis	multi-tissue	Pritchard
rs8052125	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs8052125	CLEC18A	cis	Artery Aorta	GTEx
rs8052125	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs8052125	LOC440348	cis	multi-tissue	Pritchard
rs8052125	CLEC18A	cis	Whole Blood	GTEx
rs8052125	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs8052125	LOC283970	cis	multi-tissue	Pritchard
rs8052125	CLEC18C	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70489400-70556400	Weak transcription	Stomach Mucosa	stomach
2	chr16:70512800-70556400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:70517600-70538800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr16:70518000-70545800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:70523200-70542400	Weak transcription	Hela-S3	cervix
6	chr16:70524400-70542400	Weak transcription	Fetal Brain Male	brain
7	chr16:70525600-70538200	Strong transcription	Fetal Thymus	thymus
8	chr16:70526000-70539000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr16:70528000-70553800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr16:70528800-70556400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr16:70530000-70541200	Weak transcription	Fetal Heart	heart
12	chr16:70530600-70542400	Weak transcription	HMEC	breast
13	chr16:70530600-70545800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr16:70530800-70542200	Weak transcription	K562	blood
15	chr16:70531000-70541200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr16:70531000-70542400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr16:70531000-70542800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr16:70531200-70542200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr16:70531400-70543600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr16:70531600-70542000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr16:70531600-70542800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr16:70531800-70540800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr16:70531800-70542400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr16:70531800-70542400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr16:70532000-70540000	Weak transcription	Pancreas	Pancrea
26	chr16:70532000-70540600	Weak transcription	Psoas Muscle	Psoas
27	chr16:70532000-70540800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr16:70532000-70540800	Weak transcription	Esophagus	oesophagus
29	chr16:70532000-70541000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr16:70532000-70541000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr16:70532000-70541000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr16:70532000-70541000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr16:70532000-70541200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr16:70532000-70542200	Weak transcription	HSMMtube	muscle
35	chr16:70532000-70542200	Weak transcription	HUVEC	blood vessel
36	chr16:70532000-70542200	Weak transcription	NHDF-Ad	bronchial
37	chr16:70532000-70542400	Weak transcription	Primary B cells from cord blood	blood
38	chr16:70532000-70542400	Weak transcription	Aorta	Aorta
39	chr16:70532000-70542400	Weak transcription	Fetal Lung	lung
40	chr16:70532000-70542800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr16:70532000-70543000	Weak transcription	Colonic Mucosa	Colon
42	chr16:70532000-70543000	Weak transcription	Small Intestine	intestine
43	chr16:70532000-70545600	Weak transcription	A549	lung
44	chr16:70532200-70540800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr16:70532600-70542200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr16:70533000-70538600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr16:70533000-70540600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr16:70533000-70540600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr16:70533000-70540800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr16:70533000-70541000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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