Variant report

Variant	rs647391
Chromosome Location	chr10:5951821-5951822
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:5951794-5951904	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5950213..5953065-chr10:6017303..6019683,2	MCF-7	breast:
2	chr10:5951474..5953291-chr10:5960290..5963166,2	K562	blood:
3	chr10:5946370..5949809-chr10:5950035..5953033,4	K562	blood:
4	chr10:5948073..5950157-chr10:5951295..5953499,3	MCF-7	breast:
5	chr10:5855622..5857223-chr10:5951043..5953758,2	MCF-7	breast:
6	chr10:5928731..5931390-chr10:5949628..5953556,4	K562	blood:

No data

Variant related genes	Relation type
FBXO18	TF binding region
ENSG00000272764	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000134470	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1052420	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs1707228	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2253422	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2274030	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2669124	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2669127	0.82[EUR][1000 genomes]
rs2761269	0.99[ASN][1000 genomes]
rs2942348	0.99[ASN][1000 genomes]
rs2985042	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap]
rs2985043	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2985044	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs584000	0.97[ASN][1000 genomes]
rs587620	0.99[ASN][1000 genomes]
rs587655	0.99[ASN][1000 genomes]
rs593026	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596156	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599394	0.83[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs600706	0.97[ASN][1000 genomes]
rs608197	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs609269	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs610335	0.99[ASN][1000 genomes]
rs615879	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs617165	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs622252	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs622488	0.99[ASN][1000 genomes]
rs625073	0.94[ASN][1000 genomes]
rs626040	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs627303	0.99[ASN][1000 genomes]
rs628175	0.97[ASN][1000 genomes]
rs628219	0.97[ASN][1000 genomes]
rs628234	0.97[ASN][1000 genomes]
rs628844	0.88[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs631538	0.87[ASN][1000 genomes]
rs632639	0.82[EUR][1000 genomes]
rs641034	0.81[EUR][1000 genomes]
rs644474	0.94[CEU][hapmap];0.92[CHB][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs646406	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs646490	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661411	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs662701	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs664577	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs664842	0.99[ASN][1000 genomes]
rs665364	0.91[JPT][hapmap]
rs666831	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs672219	0.87[ASN][1000 genomes]
rs672624	0.84[ASN][1000 genomes]
rs673496	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs673678	0.99[ASN][1000 genomes]
rs675416	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs679610	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682555	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs684557	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687191	0.99[ASN][1000 genomes]
rs7071536	0.84[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs7075778	0.82[EUR][1000 genomes]
rs7091817	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs792342	0.95[ASN][1000 genomes]
rs792347	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792349	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs811561	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs9329328	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9424023	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs647391	FBXO18	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5933200-5977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:5935600-5962000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr10:5936600-5952600	Weak transcription	Hela-S3	cervix
4	chr10:5936800-5953200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:5944000-5981600	Strong transcription	Fetal Intestine Small	intestine
6	chr10:5944400-5952000	Strong transcription	K562	blood
7	chr10:5944400-5955000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:5944600-5952800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr10:5944600-5981200	Strong transcription	Fetal Thymus	thymus
10	chr10:5945000-5953800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:5945800-5980800	Strong transcription	Thymus	Thymus
12	chr10:5947000-5980800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr10:5947000-5981600	Strong transcription	Placenta	Placenta
14	chr10:5947200-5981000	Strong transcription	Fetal Intestine Large	intestine
15	chr10:5947400-5970800	Strong transcription	Liver	Liver
16	chr10:5947400-5974400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr10:5947400-5981200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:5947600-5968400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:5947600-5968600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr10:5947600-5968600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr10:5947600-5975000	Strong transcription	Primary T cells from cord blood	blood
22	chr10:5947600-5981000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:5947600-5981000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr10:5947600-5981000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:5947600-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:5947600-5981200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr10:5947800-5961000	Strong transcription	Fetal Brain Female	brain
28	chr10:5947800-5974000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr10:5947800-5974400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr10:5947800-5974600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr10:5948000-5955800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:5948000-5960200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:5948000-5974600	Strong transcription	Fetal Lung	lung
34	chr10:5948000-5974800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr10:5948000-5975000	Strong transcription	Primary B cells from cord blood	blood
36	chr10:5948000-5975800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:5948200-5974000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr10:5948200-5974800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr10:5948400-5952000	Strong transcription	Fetal Stomach	stomach
40	chr10:5948400-5952400	Weak transcription	Right Atrium	heart
41	chr10:5948400-5981000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr10:5948400-5981000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr10:5948600-5952200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr10:5948600-5952400	Strong transcription	Fetal Muscle Leg	muscle
45	chr10:5948600-5981000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr10:5948800-5974200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr10:5948800-5981000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr10:5948800-5981000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr10:5948800-5981600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:5949400-5970200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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