Variant report

Variant	rs73078362
Chromosome Location	chr3:48703917-48703918
allele	C/G
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	chr3:48703363-48703957	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	chr3:48700180..48704062-chr3:48721751..48723924,3	K562	blood:
3	chr3:48701660..48704427-chr3:48712006..48713565,2	K562	blood:
4	chr3:48701937..48704062-chr3:48721900..48723446,2	K562	blood:

Variant related genes	Relation type
CELSR3	TF binding region
ENSG00000213672	Chromatin interaction
ENSG00000271973	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11557629	0.81[EUR][1000 genomes]
rs11706983	0.81[EUR][1000 genomes]
rs11708022	0.81[AMR][1000 genomes]
rs11709246	0.81[AMR][1000 genomes]
rs11713694	0.81[AMR][1000 genomes]
rs11715689	0.85[AMR][1000 genomes]
rs11715713	0.85[AMR][1000 genomes]
rs11715835	0.81[AMR][1000 genomes]
rs11719291	0.81[EUR][1000 genomes]
rs11719457	0.85[AMR][1000 genomes]
rs12715429	0.86[EUR][1000 genomes]
rs13063742	1.00[AFR][1000 genomes]
rs13069446	1.00[AFR][1000 genomes]
rs13070798	0.86[EUR][1000 genomes]
rs13073997	0.81[AMR][1000 genomes]
rs13074318	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13084000	0.81[AMR][1000 genomes]
rs13086240	0.88[AMR][1000 genomes]
rs13087930	0.81[AMR][1000 genomes]
rs13090013	0.81[EUR][1000 genomes]
rs13090839	0.85[AMR][1000 genomes]
rs13324119	0.86[EUR][1000 genomes]
rs13434258	0.81[EUR][1000 genomes]
rs17080319	0.81[EUR][1000 genomes]
rs2286651	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2286652	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2302295	0.82[EUR][1000 genomes]
rs28452701	0.86[EUR][1000 genomes]
rs28567949	0.81[EUR][1000 genomes]
rs34096717	0.86[EUR][1000 genomes]
rs34153629	0.81[EUR][1000 genomes]
rs34477108	0.81[AMR][1000 genomes]
rs34509487	0.81[AMR][1000 genomes]
rs35064573	0.81[EUR][1000 genomes]
rs35755371	1.00[AFR][1000 genomes]
rs3733086	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3821875	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67332931	0.81[AMR][1000 genomes]
rs6768448	0.82[EUR][1000 genomes]
rs68042649	0.82[EUR][1000 genomes]
rs71324924	0.81[AMR][1000 genomes]
rs73078349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9809222	0.82[EUR][1000 genomes]
rs9811027	0.81[EUR][1000 genomes]
rs9811318	0.82[EUR][1000 genomes]
rs9812200	0.80[EUR][1000 genomes]
rs9812977	0.81[EUR][1000 genomes]
rs9821797	0.82[EUR][1000 genomes]
rs9836462	0.82[EUR][1000 genomes]
rs9841602	0.82[EUR][1000 genomes]
rs9873726	0.82[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs73078362	SLC26A6	cis	lung	GTEx
rs73078362	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs73078362	WDR6	cis	Artery Tibial	GTEx
rs73078362	WDR6	cis	Esophagus Mucosa	GTEx
rs73078362	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:112 , 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	chr3:48701600-48708200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:48701600-48708400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:48701600-48708400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:48701600-48708400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:48701600-48708600	Weak transcription	Colonic Mucosa	Colon
7	chr3:48701600-48711000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:48701600-48711000	Weak transcription	Left Ventricle	heart
9	chr3:48701600-48711400	Weak transcription	Aorta	Aorta
10	chr3:48701600-48715400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:48701600-48716800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:48701600-48718000	Weak transcription	NHDF-Ad	bronchial
13	chr3:48701600-48720800	Weak transcription	Right Atrium	heart
14	chr3:48701600-48720800	Weak transcription	HUVEC	blood vessel
15	chr3:48701800-48708200	Weak transcription	Fetal Brain Female	brain
16	chr3:48701800-48708400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:48701800-48708400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:48701800-48708600	Weak transcription	Adipose Nuclei	Adipose
19	chr3:48701800-48708600	Weak transcription	Liver	Liver
20	chr3:48701800-48708600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:48701800-48708600	Weak transcription	Gastric	stomach
22	chr3:48701800-48708600	Weak transcription	Ovary	ovary
23	chr3:48701800-48709000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:48701800-48711200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:48701800-48711400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:48701800-48711400	Weak transcription	Esophagus	oesophagus
27	chr3:48701800-48711600	Weak transcription	Dnd41	blood
28	chr3:48701800-48712400	Weak transcription	Fetal Thymus	thymus
29	chr3:48701800-48713400	Weak transcription	Pancreas	Pancrea
30	chr3:48701800-48714800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:48701800-48715200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:48701800-48715200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:48701800-48715600	Weak transcription	NH-A	brain
34	chr3:48701800-48715800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:48701800-48715800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:48701800-48716800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:48701800-48721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:48702000-48707400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:48702000-48707600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:48702000-48707600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:48702000-48708000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:48702000-48708200	Weak transcription	Fetal Intestine Small	intestine
43	chr3:48702000-48708400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:48702000-48708400	Weak transcription	Brain Anterior Caudate	brain
45	chr3:48702000-48708400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:48702000-48708400	Weak transcription	Fetal Intestine Large	intestine
47	chr3:48702000-48708400	Weak transcription	A549	lung
48	chr3:48702000-48708400	Weak transcription	HSMM	muscle
49	chr3:48702000-48708600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:48702000-48708600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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