Variant report

Variant	rs73080312
Chromosome Location	chr3:48737847-48737848
allele	C/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	chr3:48737767-48738017	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:48737671-48738013	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:48737163-48738182	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:48737803-48738055	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48736950..48739890-chr3:48741169..48743085,3	K562	blood:
2	chr3:48736967..48739761-chr3:49056204..49057808,2	MCF-7	breast:
3	chr3:48735352..48738114-chr3:48738712..48740970,2	K562	blood:

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000199032	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1048940	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709092	0.80[AMR][1000 genomes]
rs11715689	0.82[AMR][1000 genomes]
rs11715713	0.82[AMR][1000 genomes]
rs11716614	0.87[AMR][1000 genomes]
rs11719457	0.82[AMR][1000 genomes]
rs13086240	0.85[AMR][1000 genomes]
rs13090839	0.82[AMR][1000 genomes]
rs56004653	0.87[AMR][1000 genomes]
rs73080361	0.87[AMR][1000 genomes]
rs9812977	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs73080312	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs73080312	WDR6	cis	Adipose Subcutaneous	GTEx
rs73080312	WDR6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
2	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
3	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
4	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
5	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:48724800-48738400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:48725000-48740800	Strong transcription	Dnd41	blood
11	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:48732800-48744800	Weak transcription	Small Intestine	intestine
14	chr3:48732800-48745400	Weak transcription	Psoas Muscle	Psoas
15	chr3:48733000-48740200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:48733000-48744800	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:48733000-48745400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
19	chr3:48733200-48738600	Strong transcription	Fetal Lung	lung
20	chr3:48733200-48738800	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:48733200-48740800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:48733200-48744000	Weak transcription	Esophagus	oesophagus
23	chr3:48733200-48746000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:48733200-48746000	Strong transcription	Fetal Intestine Small	intestine
25	chr3:48733200-48746200	Weak transcription	Right Ventricle	heart
26	chr3:48733600-48739200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:48734000-48738000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:48734000-48738600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:48734000-48746400	Weak transcription	Fetal Brain Male	brain
30	chr3:48734200-48740200	Weak transcription	Fetal Heart	heart
31	chr3:48734200-48745400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:48734400-48739800	Weak transcription	A549	lung
33	chr3:48734400-48740200	Weak transcription	NHDF-Ad	bronchial
34	chr3:48734400-48740800	Strong transcription	Fetal Intestine Large	intestine
35	chr3:48734400-48741600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:48734400-48741600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:48734400-48744600	Weak transcription	NHLF	lung
38	chr3:48734400-48745600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:48734400-48746000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:48734400-48746000	Weak transcription	Brain Substantia Nigra	brain
41	chr3:48734400-48746200	Weak transcription	Gastric	stomach
42	chr3:48734400-48746400	Weak transcription	Stomach Mucosa	stomach
43	chr3:48734400-48748800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:48734800-48738000	Strong transcription	NHEK	skin
45	chr3:48734800-48740800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:48735000-48738200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr3:48735200-48738800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:48735200-48738800	Strong transcription	Placenta	Placenta
49	chr3:48735200-48740600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr3:48735400-48738000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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