Variant report

Variant	rs2793799
Chromosome Location	chr1:179202209-179202210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179198432..179201318-chr1:179202068..179205329,4	K562	blood:
2	chr1:179198171..179200339-chr1:179200628..179202666,2	MCF-7	breast:
3	chr1:179198578..179200857-chr1:179201738..179204176,2	K562	blood:
4	chr1:179050126..179052698-chr1:179201088..179202992,3	K562	blood:
5	chr1:179202041..179203802-chr1:179206538..179208107,2	K562	blood:
6	chr1:179194698..179198189-chr1:179199454..179203395,4	K562	blood:

Variant related genes	Relation type
ENSG00000186283	Chromatin interaction
ENSG00000143322	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1046385	0.85[JPT][hapmap]
rs1078872	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs10798652	0.95[JPT][hapmap]
rs10913690	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs10913695	0.89[EUR][1000 genomes]
rs10913697	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1173077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12130276	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1325194	0.81[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap]
rs1325195	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs17362081	0.80[JPT][hapmap]
rs1856967	0.90[EUR][1000 genomes]
rs1856968	0.92[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1858551	0.89[EUR][1000 genomes]
rs2066279	1.00[CEU][hapmap];0.83[JPT][hapmap];0.98[EUR][1000 genomes]
rs2087559	0.93[EUR][1000 genomes]
rs2130576	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs2171959	1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];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	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2636265	0.98[EUR][1000 genomes]
rs2636266	0.81[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs2636274	1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2636276	0.81[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2636280	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs2636281	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636282	0.99[EUR][1000 genomes]
rs2636287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes]
rs2636290	0.95[GIH][hapmap];0.81[JPT][hapmap]
rs2791940	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs2791941	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];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	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs2793797	0.81[ASW][hapmap];0.92[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2793798	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs2793803	1.00[CEU][hapmap];0.82[JPT][hapmap];0.99[EUR][1000 genomes]
rs2793805	0.81[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap]
rs2793806	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793812	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs2793816	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs2816167	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816183	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs2816185	0.90[EUR][1000 genomes]
rs2816186	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2816187	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs2816189	0.92[EUR][1000 genomes]
rs2816196	0.90[EUR][1000 genomes]
rs2816197	0.93[EUR][1000 genomes]
rs2816198	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes]
rs2816199	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes]
rs2816201	0.82[JPT][hapmap]
rs2816202	0.94[EUR][1000 genomes]
rs2816203	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs2816204	0.94[EUR][1000 genomes]
rs2816206	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816208	0.98[EUR][1000 genomes]
rs2816209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816210	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816211	0.99[EUR][1000 genomes]
rs2816213	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap]
rs2816214	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs3210839	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs36122838	0.87[EUR][1000 genomes]
rs377785	0.98[EUR][1000 genomes]
rs3813642	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs3813643	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs3818433	0.95[GIH][hapmap];0.80[TSI][hapmap]
rs411266	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs434283	0.98[EUR][1000 genomes]
rs451088	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs4651012	0.87[EUR][1000 genomes]
rs4651013	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs4651014	0.81[JPT][hapmap]
rs915337	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs931441	0.81[JPT][hapmap]
rs965401	0.92[EUR][1000 genomes]
rs9726961	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs9727252	0.89[EUR][1000 genomes]
rs9728480	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2793799	FAM20B	cis	parietal	SCAN
rs2793799	FAM20B	cis	lymphoblastoid	seeQTL
rs2793799	TOR3A	cis	Artery Tibial	GTEx
rs2793799	IER5	cis	cerebellum	SCAN
rs2793799	ABL2	cis	parietal	SCAN

Chromatin state (count:23 , 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	chr1:179199600-179203000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:179199800-179204600	Enhancers	Hela-S3	cervix
4	chr1:179200200-179202400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:179200200-179203000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:179200200-179203000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:179201200-179202800	Enhancers	NH-A	brain
8	chr1:179201200-179203000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:179201200-179204400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:179201200-179204400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:179201200-179204600	Enhancers	HMEC	breast
12	chr1:179201200-179204600	Enhancers	NHEK	skin
13	chr1:179201600-179202400	Enhancers	A549	lung
14	chr1:179201600-179202400	Weak transcription	HSMM	muscle
15	chr1:179201600-179202600	Weak transcription	HUVEC	blood vessel
16	chr1:179201600-179202600	Weak transcription	NHLF	lung
17	chr1:179201600-179203000	Weak transcription	NHDF-Ad	bronchial
18	chr1:179201600-179203000	Weak transcription	Osteobl	bone
19	chr1:179201600-179203600	Weak transcription	HepG2	liver
20	chr1:179201600-179203600	Weak transcription	K562	blood
21	chr1:179201800-179203600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:179201800-179203600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:179202000-179202600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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