Variant report

Variant	rs12715429
Chromosome Location	chr3:48709246-48709247
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48709183-48709255	K562	blood:	n/a	n/a
2	POLR2A	chr3:48707067-48710338	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48708773-48709395	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48698129..48704726-chr3:48706101..48715056,13	MCF-7	breast:
2	chr3:48707451..48709313-chr3:49057403..49059390,2	MCF-7	breast:
3	chr3:48708844..48711305-chr3:48727090..48731325,3	K562	blood:

Variant related genes	Relation type
ENSG00000271973	TF binding region
ENSG00000178149	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000228350	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11557629	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11706203	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11706983	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11708786	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11715177	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11719291	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12107252	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12107418	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13063223	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13063312	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13070798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076269	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090013	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13096357	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13316551	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13324119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324142	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13324950	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13434258	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17080319	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2276850	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2276852	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286651	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286652	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302295	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2310996	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2310997	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28452701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28567949	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28657585	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28793701	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34096717	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34153629	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34368826	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34577723	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34638686	0.84[EUR][1000 genomes]
rs35064573	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3733086	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806694	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821875	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821876	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4077495	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56735597	0.87[AMR][1000 genomes]
rs57334642	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768448	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773261	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68042649	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73078349	0.82[EUR][1000 genomes]
rs73078362	0.86[EUR][1000 genomes]
rs740787	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7620853	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631574	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9809222	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811027	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9811318	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812200	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812977	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9821797	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834996	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9836462	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841602	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854034	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9868809	0.85[EUR][1000 genomes]
rs9873726	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877542	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9877685	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9878063	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9882549	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv876763	chr3:48669648-48710310	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12715429	WDR6	cis	Whole Blood	GTEx
rs12715429	WDR6	cis	Esophagus Mucosa	GTEx
rs12715429	WDR6	cis	lung	GTEx
rs12715429	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs12715429	WDR6	cis	Artery Tibial	GTEx
rs12715429	SLC26A6	cis	lung	GTEx
rs12715429	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48701200-48721000	Weak transcription	Fetal Brain Male	brain
2	chr3:48701600-48711000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:48701600-48711000	Weak transcription	Left Ventricle	heart
4	chr3:48701600-48711400	Weak transcription	Aorta	Aorta
5	chr3:48701600-48715400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:48701600-48716800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:48701600-48718000	Weak transcription	NHDF-Ad	bronchial
8	chr3:48701600-48720800	Weak transcription	Right Atrium	heart
9	chr3:48701600-48720800	Weak transcription	HUVEC	blood vessel
10	chr3:48701800-48711200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:48701800-48711400	Weak transcription	Brain Substantia Nigra	brain
12	chr3:48701800-48711400	Weak transcription	Esophagus	oesophagus
13	chr3:48701800-48711600	Weak transcription	Dnd41	blood
14	chr3:48701800-48712400	Weak transcription	Fetal Thymus	thymus
15	chr3:48701800-48713400	Weak transcription	Pancreas	Pancrea
16	chr3:48701800-48714800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:48701800-48715200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:48701800-48715200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:48701800-48715600	Weak transcription	NH-A	brain
20	chr3:48701800-48715800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:48701800-48715800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:48701800-48716800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:48701800-48721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:48702000-48711200	Weak transcription	HMEC	breast
25	chr3:48702000-48711400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:48702000-48711400	Weak transcription	Placenta	Placenta
27	chr3:48702000-48711400	Weak transcription	GM12878-XiMat	blood
28	chr3:48702000-48712000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:48702000-48712000	Weak transcription	Thymus	Thymus
30	chr3:48702000-48712000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:48702000-48712200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:48702000-48712400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:48702000-48712400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:48702000-48716800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:48702000-48716800	Weak transcription	HSMMtube	muscle
36	chr3:48702000-48721400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:48702200-48711400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:48702200-48712000	Weak transcription	HepG2	liver
39	chr3:48702200-48717000	Weak transcription	K562	blood
40	chr3:48702600-48711600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:48702600-48715000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:48702800-48711400	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:48702800-48714800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:48702800-48717000	Weak transcription	Fetal Heart	heart
45	chr3:48703200-48711000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:48703200-48711000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:48703200-48711400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:48703200-48711400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:48703200-48711800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:48703200-48715200	Weak transcription	Stomach Mucosa	stomach

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