Variant report

Variant	rs9848203
Chromosome Location	chr3:48753149-48753150
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	chr3:48752668-48753272	H1-hESC	embryonic stem cell:	n/a	n/a
2	RFX5	chr3:48752360-48753452	SK-N-SH	brain:	n/a	chr3:48752786-48752800
3	MAZ	chr3:48752707-48755155	IMR90	lung:	n/a	n/a
4	REST	chr3:48752144-48755489	H1-neurons	neurons:	n/a	chr3:48754666-48754679 chr3:48754900-48754913
5	RFX5	chr3:48752407-48753435	IMR90	lung:	n/a	chr3:48752786-48752800
6	ZNF384	chr3:48753074-48753274	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48753119..48755656-chr3:48955067..48957607,2	MCF-7	breast:
2	chr3:48752504..48754633-chr3:49057932..49060797,2	K562	blood:

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000221883	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000207605	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10865952	0.87[ASN][1000 genomes]
rs11557629	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706203	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11706983	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11708786	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715177	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719291	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493578	0.87[ASN][1000 genomes]
rs12497850	0.87[ASN][1000 genomes]
rs13063223	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13090013	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13316551	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13324950	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13434258	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1352420	0.87[ASN][1000 genomes]
rs17080319	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28567949	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28657585	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28793701	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34153629	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34577723	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35064573	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4077495	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858798	0.87[ASN][1000 genomes]
rs4858828	0.87[ASN][1000 genomes]
rs4858831	0.87[ASN][1000 genomes]
rs56735597	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61137521	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788650	0.87[ASN][1000 genomes]
rs9811027	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9834996	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854034	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9877542	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9877685	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9882549	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

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

SNP	Gene	Cis/trans	Tissue	Source
rs9848203	WDR6	cis	Adipose Subcutaneous	GTEx
rs9848203	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
2	chr3:48740000-48753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:48745800-48753400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:48749400-48753400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:48750000-48753200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:48750000-48753200	Genic enhancers	Placenta	Placenta
7	chr3:48751000-48753400	Weak transcription	Ovary	ovary
8	chr3:48751000-48753800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:48751000-48754000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48751000-48754000	Weak transcription	Gastric	stomach
11	chr3:48751200-48755000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr3:48751800-48753200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:48752000-48753200	Genic enhancers	Liver	Liver
14	chr3:48752000-48754000	Weak transcription	Esophagus	oesophagus
15	chr3:48752200-48753200	Flanking Active TSS	HMEC	breast
16	chr3:48752400-48753200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
17	chr3:48752400-48753200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:48752400-48753200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:48752400-48753200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr3:48752400-48753200	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr3:48752400-48753400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:48752400-48753400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr3:48752600-48753200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:48752600-48753200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
25	chr3:48752600-48753200	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
26	chr3:48752600-48753200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:48752600-48753200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr3:48752600-48753200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:48752600-48753200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:48752600-48753200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
31	chr3:48752600-48753200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
32	chr3:48752600-48753200	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr3:48752600-48753200	Flanking Active TSS	HSMMtube	muscle
34	chr3:48752600-48753200	Transcr. at gene 5' and 3'	NHEK	skin
35	chr3:48752600-48753200	Flanking Active TSS	NHLF	lung
36	chr3:48752600-48753400	Transcr. at gene 5' and 3'	K562	blood
37	chr3:48752600-48753600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
38	chr3:48752600-48753600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr3:48752600-48753800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr3:48752600-48753800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr3:48752600-48754400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr3:48752800-48753200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:48752800-48753200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:48752800-48753200	Flanking Active TSS	A549	lung
45	chr3:48752800-48753400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:48752800-48753400	Transcr. at gene 5' and 3'	Fetal Brain Male	brain
47	chr3:48752800-48753400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr3:48752800-48753400	Flanking Active TSS	HepG2	liver
49	chr3:48752800-48753400	Flanking Active TSS	NH-A	brain
50	chr3:48752800-48753400	Flanking Active TSS	Osteobl	bone

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