Variant report

Variant	rs9854034
Chromosome Location	chr3:48733507-48733508
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	chr3:48733439-48734449	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:48733360-48733549	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48733494-48734462	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48699225..48701604-chr3:48731929..48734312,2	MCF-7	breast:
2	chr3:48732542..48735376-chr3:48750993..48752883,2	K562	blood:
3	chr3:48730035..48731678-chr3:48732538..48734765,2	MCF-7	breast:

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000068745	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10865952	0.92[ASN][1000 genomes]
rs11557629	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11706203	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11706983	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708786	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715177	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719291	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493578	0.92[ASN][1000 genomes]
rs12497850	0.92[ASN][1000 genomes]
rs12715429	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13063223	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13070798	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13090013	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13316551	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13324119	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13324950	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13434258	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1352420	0.92[ASN][1000 genomes]
rs17080319	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286651	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2286652	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2302295	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28452701	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28567949	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28657585	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28793701	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34096717	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34153629	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34577723	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35064573	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733086	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3821875	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4077495	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858798	0.92[ASN][1000 genomes]
rs4858828	0.92[ASN][1000 genomes]
rs4858831	0.92[ASN][1000 genomes]
rs56735597	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61137521	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768448	0.82[EUR][1000 genomes]
rs6788650	0.92[ASN][1000 genomes]
rs68042649	0.82[EUR][1000 genomes]
rs7633840	0.84[ASN][1000 genomes]
rs9809222	0.82[EUR][1000 genomes]
rs9811027	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811318	0.82[EUR][1000 genomes]
rs9812977	0.83[EUR][1000 genomes]
rs9821797	0.82[EUR][1000 genomes]
rs9834996	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9836462	0.82[EUR][1000 genomes]
rs9841602	0.82[EUR][1000 genomes]
rs9848203	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9873726	0.82[EUR][1000 genomes]
rs9877542	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877685	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9882549	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9854034	WDR6	cis	lung	GTEx
rs9854034	WDR6	cis	Adipose Subcutaneous	GTEx
rs9854034	WDR6	cis	Esophagus Mucosa	GTEx
rs9854034	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9854034	WDR6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48723800-48733800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
3	chr3:48724600-48734000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:48724600-48734000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
6	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
7	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
8	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
9	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48724800-48733800	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:48724800-48733800	Strong transcription	HepG2	liver
12	chr3:48724800-48734000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:48724800-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:48724800-48737600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:48724800-48738400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:48725000-48740800	Strong transcription	Dnd41	blood
20	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:48730600-48733600	Weak transcription	K562	blood
23	chr3:48731000-48734000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:48731200-48735000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:48731400-48734400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:48731800-48733800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:48732000-48734400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:48732000-48734400	Genic enhancers	A549	lung
29	chr3:48732200-48734400	Genic enhancers	Fetal Kidney	kidney
30	chr3:48732200-48735200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:48732400-48733600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:48732400-48734400	Genic enhancers	Fetal Intestine Large	intestine
33	chr3:48732400-48736400	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr3:48732600-48733800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:48732600-48734400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:48732800-48733800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:48732800-48733800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr3:48732800-48734200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:48732800-48734200	Genic enhancers	HUVEC	blood vessel
40	chr3:48732800-48734400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:48732800-48734400	Enhancers	Pancreas	Pancrea
42	chr3:48732800-48734400	Enhancers	Stomach Mucosa	stomach
43	chr3:48732800-48734400	Genic enhancers	NHEK	skin
44	chr3:48732800-48735400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:48732800-48744800	Weak transcription	Small Intestine	intestine
46	chr3:48732800-48745400	Weak transcription	Psoas Muscle	Psoas
47	chr3:48733000-48733600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:48733000-48733600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr3:48733000-48733600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:48733000-48733600	Enhancers	Hela-S3	cervix

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