Variant report

Variant	rs2793803
Chromosome Location	chr1:179201438-179201439
allele	G/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	GATA2	chr1:179201063-179201484	HUVEC	blood vessel:	n/a	chr1:179201291-179201302
2	CEBPB	chr1:179201100-179201441	Hela-S3	cervix:	n/a	chr1:179201328-179201345
3	BHLHE40	chr1:179201098-179201538	K562	blood:	n/a	n/a
4	CEBPB	chr1:179201136-179201448	A549	lung:	n/a	chr1:179201328-179201345
5	GATA3	chr1:179201059-179201566	SK-N-SH	brain:	n/a	chr1:179201291-179201302
6	GATA3	chr1:179200974-179201585	SK-N-SH	brain:	n/a	chr1:179201291-179201302
7	FOXA1	chr1:179201136-179201488	HepG2	liver:	n/a	n/a
8	SP1	chr1:179201070-179201549	A549	lung:	n/a	n/a
9	FOXA2	chr1:179201151-179201472	HepG2	liver:	n/a	n/a
10	FOXA1	chr1:179201138-179201509	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179198171..179200339-chr1:179200628..179202666,2	MCF-7	breast:
2	chr1:179050126..179052698-chr1:179201088..179202992,3	K562	blood:
3	chr1:179194698..179198189-chr1:179199454..179203395,4	K562	blood:

Variant related genes	Relation type
ABL2	TF binding region
ENSG00000143322	Chromatin interaction
ENSG00000186283	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1078872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913690	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs10913692	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10913695	0.91[EUR][1000 genomes]
rs10913697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1173077	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs12130276	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs1325195	0.88[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs1763022	0.91[ASN][1000 genomes]
rs1807916	0.88[ASN][1000 genomes]
rs1826183	0.88[ASN][1000 genomes]
rs1856967	0.89[EUR][1000 genomes]
rs1856968	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1858551	0.91[EUR][1000 genomes]
rs2050923	0.92[ASN][1000 genomes]
rs2066279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2087559	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2130576	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2171958	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2171959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2258217	0.91[EUR][1000 genomes]
rs2258221	0.89[EUR][1000 genomes]
rs2306941	0.88[ASN][1000 genomes]
rs2486995	0.91[EUR][1000 genomes]
rs2486997	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2487563	0.92[ASN][1000 genomes]
rs2493124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2636265	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636272	0.89[ASN][1000 genomes]
rs2636274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2636276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2636277	0.95[CHB][hapmap]
rs2636280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636281	0.99[EUR][1000 genomes]
rs2636282	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636287	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs2636293	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2791940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2791941	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2791942	0.81[EUR][1000 genomes]
rs2791943	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2791944	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2793790	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2793793	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2793795	0.85[EUR][1000 genomes]
rs2793796	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes]
rs2793797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2793798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes]
rs2793799	1.00[CEU][hapmap];0.82[JPT][hapmap];0.99[EUR][1000 genomes]
rs2793800	0.82[ASN][1000 genomes]
rs2793801	0.90[ASN][1000 genomes]
rs2793802	0.92[ASN][1000 genomes]
rs2793806	0.95[EUR][1000 genomes]
rs2793810	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2793812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793813	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2793816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2816166	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816167	0.99[EUR][1000 genomes]
rs2816168	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2816183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2816184	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816185	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2816186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2816187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs2816189	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2816190	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816191	0.81[ASN][1000 genomes]
rs2816193	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816196	0.91[EUR][1000 genomes]
rs2816197	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816200	0.85[ASN][1000 genomes]
rs2816201	0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816202	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816204	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816206	0.98[EUR][1000 genomes]
rs2816207	0.91[ASN][1000 genomes]
rs2816208	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816209	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs2816210	0.96[EUR][1000 genomes]
rs2816211	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816212	0.89[ASN][1000 genomes]
rs2816213	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2816214	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816218	0.96[CHB][hapmap];0.91[ASN][1000 genomes]
rs3121198	0.84[ASN][1000 genomes]
rs3122376	0.86[ASN][1000 genomes]
rs3210839	0.96[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs36122838	0.88[EUR][1000 genomes]
rs377785	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3813643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3829794	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs411266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs413613	0.90[ASN][1000 genomes]
rs434283	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs451088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4651012	0.88[EUR][1000 genomes]
rs4651013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6668200	0.92[YRI][hapmap]
rs915337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425839	0.91[ASN][1000 genomes]
rs965401	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9662858	0.96[CHB][hapmap];0.83[JPT][hapmap]
rs9726961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9727252	0.91[EUR][1000 genomes]
rs9728480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9729199	0.88[EUR][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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2793803	TOR3A	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179199400-179210000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:179199600-179201800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:179199600-179203000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:179199800-179201600	Enhancers	HepG2	liver
5	chr1:179199800-179201600	Enhancers	HUVEC	blood vessel
6	chr1:179199800-179204600	Enhancers	Hela-S3	cervix
7	chr1:179200000-179201600	Enhancers	NHLF	lung
8	chr1:179200000-179201800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:179200200-179201600	Enhancers	K562	blood
10	chr1:179200200-179202400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:179200200-179203000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:179200200-179203000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:179201200-179201600	Flanking Active TSS	A549	lung
14	chr1:179201200-179201600	Enhancers	NHDF-Ad	bronchial
15	chr1:179201200-179201600	Enhancers	Osteobl	bone
16	chr1:179201200-179202200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:179201200-179202800	Enhancers	NH-A	brain
18	chr1:179201200-179203000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:179201200-179204400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:179201200-179204400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:179201200-179204600	Enhancers	HMEC	breast
22	chr1:179201200-179204600	Enhancers	NHEK	skin
23	chr1:179201400-179201600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:179201400-179201600	Enhancers	HSMM	muscle
25	chr1:179201400-179202000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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