Variant report

Variant	rs668498
Chromosome Location	chr10:5958072-5958073
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	chr10:5958066-5958226	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:5957299..5960172-chr10:5961811..5965784,4	K562	blood:
2	chr10:5930440..5932910-chr10:5957697..5960803,4	MCF-7	breast:
3	chr10:5957022..5959868-chr10:5961811..5965784,4	K562	blood:
4	chr10:5958041..5960183-chr10:5985968..5987908,2	K562	blood:

Variant related genes	Relation type
FBXO18	TF binding region
ENSG00000134461	Chromatin interaction
ENSG00000232807	Chromatin interaction
ENSG00000134452	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2274029	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs2320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2669122	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2669126	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4293039	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs582359	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591510	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591878	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs593610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs595923	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598331	0.92[ASN][1000 genomes]
rs603780	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs607728	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs621628	0.97[ASN][1000 genomes]
rs622758	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs626344	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs633797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs633928	0.98[ASN][1000 genomes]
rs633930	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs635532	0.98[ASN][1000 genomes]
rs636578	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs647945	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs649537	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs664603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs670856	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs672126	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs680020	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs685852	0.98[ASN][1000 genomes]
rs686854	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs688388	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs792348	0.83[ASN][1000 genomes]
rs907687	0.84[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs980230	0.84[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]

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

No data

Chromatin state (count:125 , 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	chr10:5944000-5981600	Strong transcription	Fetal Intestine Small	intestine
4	chr10:5944600-5981200	Strong transcription	Fetal Thymus	thymus
5	chr10:5945800-5980800	Strong transcription	Thymus	Thymus
6	chr10:5947000-5980800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr10:5947000-5981600	Strong transcription	Placenta	Placenta
8	chr10:5947200-5981000	Strong transcription	Fetal Intestine Large	intestine
9	chr10:5947400-5970800	Strong transcription	Liver	Liver
10	chr10:5947400-5974400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr10:5947400-5981200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr10:5947600-5968400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr10:5947600-5968600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr10:5947600-5968600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr10:5947600-5975000	Strong transcription	Primary T cells from cord blood	blood
16	chr10:5947600-5981000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:5947600-5981000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr10:5947600-5981000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr10:5947600-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:5947600-5981200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr10:5947800-5961000	Strong transcription	Fetal Brain Female	brain
22	chr10:5947800-5974000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:5947800-5974400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr10:5947800-5974600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr10:5948000-5960200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr10:5948000-5974600	Strong transcription	Fetal Lung	lung
27	chr10:5948000-5974800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr10:5948000-5975000	Strong transcription	Primary B cells from cord blood	blood
29	chr10:5948000-5975800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr10:5948200-5974000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr10:5948200-5974800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr10:5948400-5981000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr10:5948400-5981000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr10:5948600-5981000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr10:5948800-5974200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr10:5948800-5981000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:5948800-5981000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr10:5948800-5981600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr10:5949400-5970200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:5949600-5960600	Strong transcription	NHLF	lung
41	chr10:5949600-5975600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr10:5949800-5960800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr10:5949800-5967200	Strong transcription	Adipose Nuclei	Adipose
44	chr10:5949800-5973400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:5949800-5975000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr10:5950000-5976400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr10:5950000-5980400	Strong transcription	Dnd41	blood
48	chr10:5950200-5975800	Strong transcription	Brain Germinal Matrix	brain
49	chr10:5950200-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr10:5950600-5959800	Strong transcription	NHEK	skin

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