Variant report

Variant	rs4600794
Chromosome Location	chr3:146184187-146184188
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146139318..146141303-chr3:146183434..146185764,2	MCF-7	breast:
2	chr3:146176309..146178627-chr3:146183394..146185507,2	K562	blood:

Variant related genes	Relation type
ENSG00000163746	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10804713	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10804714	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10935626	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10935631	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10935632	1.00[CHB][hapmap]
rs11720256	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12053987	0.94[ASN][1000 genomes]
rs12054302	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12054308	0.94[ASN][1000 genomes]
rs12054453	0.81[ASN][1000 genomes]
rs12054455	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12107218	0.81[ASN][1000 genomes]
rs12486656	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12486737	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12487546	1.00[CHB][hapmap]
rs12487572	0.86[ASN][1000 genomes]
rs12492503	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12494007	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs12494206	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12629356	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12629420	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12633694	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];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068178	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13068800	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13081634	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13088225	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs13090489	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs13092702	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1403641	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs1403642	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1403643	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1403644	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1403645	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1523334	0.84[ASN][1000 genomes]
rs1523335	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1523336	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1608389	0.85[ASN][1000 genomes]
rs1608390	0.83[ASN][1000 genomes]
rs1608391	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs1608392	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs17351881	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2037565	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2091064	0.84[ASN][1000 genomes]
rs2222465	0.85[ASN][1000 genomes]
rs2222466	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2868436	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2868438	0.83[ASN][1000 genomes]
rs34198003	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34359311	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34535967	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34740686	0.85[ASN][1000 genomes]
rs35082616	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35223042	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35336826	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35374128	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35695439	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4234358	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4282029	0.91[ASN][1000 genomes]
rs4333063	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4334615	0.85[ASN][1000 genomes]
rs4355250	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4380387	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4444684	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4476473	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4558726	0.81[ASN][1000 genomes]
rs4569626	0.95[ASN][1000 genomes]
rs4572737	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs4597678	0.85[ASN][1000 genomes]
rs4681119	1.00[CHB][hapmap]
rs4681120	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4681318	0.89[ASN][1000 genomes]
rs4681319	0.94[ASN][1000 genomes]
rs4681320	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4681321	0.94[ASN][1000 genomes]
rs4681322	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4681326	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs473517	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs506791	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs509382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533756	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs535344	0.86[ASN][1000 genomes]
rs544043	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544979	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs570781	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs574318	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57545585	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6440429	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6440430	0.94[ASN][1000 genomes]
rs6440432	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6440435	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6766583	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6766800	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6767156	1.00[CHB][hapmap]
rs6774338	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6798352	0.84[ASN][1000 genomes]
rs6801846	0.81[ASN][1000 genomes]
rs6801964	0.81[ASN][1000 genomes]
rs6806369	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6806535	0.88[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.86[YRI][hapmap]
rs692749	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7434147	0.81[ASN][1000 genomes]
rs7434212	0.93[ASN][1000 genomes]
rs7614557	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7617214	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs7620107	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7628445	0.94[ASN][1000 genomes]
rs7633474	0.81[ASN][1000 genomes]
rs7645939	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs7646988	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7650361	0.94[ASN][1000 genomes]
rs7650546	0.82[ASN][1000 genomes]
rs7653701	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs940193	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs955611	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877618	chr3:146096182-146192324	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv877622	chr3:146131961-146219740	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4600794	MXRA7	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146181600-146185000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:146181600-146185200	Enhancers	NHDF-Ad	bronchial
3	chr3:146181600-146185800	Weak transcription	K562	blood
4	chr3:146181600-146187000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:146181800-146185000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:146182400-146185200	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr3:146182600-146184200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:146182600-146185200	Enhancers	A549	lung
9	chr3:146182600-146186000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:146183000-146186200	Weak transcription	Fetal Stomach	stomach
11	chr3:146183000-146187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:146183000-146187000	Weak transcription	HMEC	breast
13	chr3:146183000-146187000	Weak transcription	NHEK	skin
14	chr3:146183400-146185800	Weak transcription	Fetal Heart	heart
15	chr3:146183600-146184200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr3:146183600-146186000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:146183600-146187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:146183800-146185400	Enhancers	NHLF	lung
19	chr3:146184000-146184200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:146184000-146184200	Enhancers	Aorta	Aorta
21	chr3:146184000-146184200	Enhancers	Esophagus	oesophagus
22	chr3:146184000-146184200	ZNF genes & repeats	Pancreas	Pancrea
23	chr3:146184000-146184800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr3:146184000-146185000	Enhancers	Hela-S3	cervix
25	chr3:146184000-146185200	Enhancers	Osteobl	bone
26	chr3:146184000-146186200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:146184000-146187000	Weak transcription	Right Atrium	heart

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