Variant report

Variant	rs2816167
Chromosome Location	chr1:179200657-179200658
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179189295..179193775-chr1:179196197..179201101,5	K562	blood:
2	chr1:179198171..179200339-chr1:179200628..179202666,2	MCF-7	breast:
3	chr1:179187242..179191261-chr1:179196503..179201085,5	MCF-7	breast:
4	chr1:179194698..179198189-chr1:179199454..179203395,4	K562	blood:

Variant related genes	Relation type
ENSG00000143322	Chromatin interaction
ENSG00000225711	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10157885	0.80[AFR][1000 genomes]
rs1078872	0.98[EUR][1000 genomes]
rs10913690	0.86[EUR][1000 genomes]
rs10913695	0.89[EUR][1000 genomes]
rs10913697	0.89[EUR][1000 genomes]
rs1173077	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12130276	0.89[EUR][1000 genomes]
rs1856967	0.90[EUR][1000 genomes]
rs1856968	0.89[EUR][1000 genomes]
rs1858551	0.89[EUR][1000 genomes]
rs2066279	0.98[EUR][1000 genomes]
rs2087559	0.93[EUR][1000 genomes]
rs2130576	0.98[EUR][1000 genomes]
rs2171959	0.89[EUR][1000 genomes]
rs2258217	0.91[EUR][1000 genomes]
rs2258221	0.88[EUR][1000 genomes]
rs2486995	0.89[EUR][1000 genomes]
rs2486997	0.89[EUR][1000 genomes]
rs2493124	0.89[EUR][1000 genomes]
rs2636265	0.98[EUR][1000 genomes]
rs2636266	0.81[AMR][1000 genomes]
rs2636274	0.91[EUR][1000 genomes]
rs2636276	0.92[EUR][1000 genomes]
rs2636280	0.94[EUR][1000 genomes]
rs2636281	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636282	0.99[EUR][1000 genomes]
rs2636287	0.92[EUR][1000 genomes]
rs2636289	0.81[AMR][1000 genomes]
rs2791940	0.91[EUR][1000 genomes]
rs2791941	0.92[EUR][1000 genomes]
rs2791942	0.80[EUR][1000 genomes]
rs2791943	0.91[EUR][1000 genomes]
rs2793793	0.93[EUR][1000 genomes]
rs2793795	0.84[EUR][1000 genomes]
rs2793796	0.90[EUR][1000 genomes]
rs2793797	0.89[EUR][1000 genomes]
rs2793798	0.89[EUR][1000 genomes]
rs2793799	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793803	0.99[EUR][1000 genomes]
rs2793804	0.81[AMR][1000 genomes]
rs2793805	0.81[AMR][1000 genomes]
rs2793806	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793807	0.81[AMR][1000 genomes]
rs2793812	0.94[EUR][1000 genomes]
rs2816183	0.91[EUR][1000 genomes]
rs2816185	0.90[EUR][1000 genomes]
rs2816186	0.92[EUR][1000 genomes]
rs2816187	0.90[EUR][1000 genomes]
rs2816189	0.92[EUR][1000 genomes]
rs2816196	0.90[EUR][1000 genomes]
rs2816197	0.93[EUR][1000 genomes]
rs2816198	0.94[EUR][1000 genomes]
rs2816199	0.94[EUR][1000 genomes]
rs2816202	0.94[EUR][1000 genomes]
rs2816203	0.94[EUR][1000 genomes]
rs2816204	0.94[EUR][1000 genomes]
rs2816206	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816208	0.98[EUR][1000 genomes]
rs2816209	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816210	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816211	0.99[EUR][1000 genomes]
rs2816214	0.98[EUR][1000 genomes]
rs28459842	0.85[AFR][1000 genomes]
rs3210839	0.87[EUR][1000 genomes]
rs36122838	0.87[EUR][1000 genomes]
rs377785	0.98[EUR][1000 genomes]
rs3813642	0.86[EUR][1000 genomes]
rs3813643	0.86[EUR][1000 genomes]
rs411266	0.98[EUR][1000 genomes]
rs434283	0.98[EUR][1000 genomes]
rs451088	0.98[EUR][1000 genomes]
rs4651012	0.87[EUR][1000 genomes]
rs4651013	0.87[EUR][1000 genomes]
rs55642919	0.80[AFR][1000 genomes]
rs55955319	0.85[AFR][1000 genomes]
rs61821690	0.81[AMR][1000 genomes]
rs915337	0.98[EUR][1000 genomes]
rs931441	0.81[AMR][1000 genomes]
rs965401	0.92[EUR][1000 genomes]
rs9726961	0.89[EUR][1000 genomes]
rs9727252	0.89[EUR][1000 genomes]
rs9728480	0.89[EUR][1000 genomes]
rs9729199	0.87[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
rs2816167	TOR3A	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179199400-179201400	Weak transcription	HSMM	muscle
2	chr1:179199400-179210000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:179199600-179201400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:179199600-179201800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:179199600-179203000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:179199800-179201600	Enhancers	HepG2	liver
7	chr1:179199800-179201600	Enhancers	HUVEC	blood vessel
8	chr1:179199800-179204600	Enhancers	Hela-S3	cervix
9	chr1:179200000-179201600	Enhancers	NHLF	lung
10	chr1:179200000-179201800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:179200200-179200800	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr1:179200200-179201200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:179200200-179201200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:179200200-179201200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:179200200-179201200	Enhancers	A549	lung
16	chr1:179200200-179201200	Weak transcription	HMEC	breast
17	chr1:179200200-179201200	Weak transcription	NH-A	brain
18	chr1:179200200-179201200	Weak transcription	NHDF-Ad	bronchial
19	chr1:179200200-179201200	Weak transcription	NHEK	skin
20	chr1:179200200-179201200	Weak transcription	Osteobl	bone
21	chr1:179200200-179201600	Enhancers	K562	blood
22	chr1:179200200-179202400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:179200200-179203000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:179200200-179203000	Weak transcription	Muscle Satellite Cultured Cells	--

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