Variant report

Variant	rs613519
Chromosome Location	chr3:52468940-52468941
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52467987..52470484-chr3:52476648..52478461,2	K562	blood:
2	chr3:52468739..52471066-chr3:52488025..52490094,2	K562	blood:
3	chr3:52468021..52470813-chr3:52473930..52477300,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010322	Chromatin interaction
ENSG00000114854	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs1011063	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1011064	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1035002	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1035003	0.81[EUR][1000 genomes]
rs1077142	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10865972	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11721286	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs123598	1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs123602	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs123603	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs13065677	0.83[AMR][1000 genomes]
rs13071708	1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs13074649	0.81[EUR][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs13076890	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13089892	0.82[MEX][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13091360	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13091545	1.00[JPT][hapmap]
rs13096571	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13098856	0.83[AMR][1000 genomes]
rs1541495	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2109557	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109558	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109559	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2159607	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2215466	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2335640	1.00[JPT][hapmap]
rs2335929	0.81[EUR][1000 genomes]
rs28481563	0.92[ASN][1000 genomes]
rs2878549	1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[EUR][1000 genomes]
rs34181173	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34332947	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs34628357	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs34827613	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35130772	0.83[AMR][1000 genomes]
rs353548	1.00[JPT][hapmap]
rs35860312	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35982798	0.81[EUR][1000 genomes]
rs3755810	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3774409	1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796342	0.83[AMR][1000 genomes]
rs3796343	1.00[JPT][hapmap]
rs390802	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs409803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419050	1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs419604	1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs419752	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4312651	1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs4687541	0.81[EUR][1000 genomes]
rs4687543	0.81[EUR][1000 genomes]
rs4687544	0.81[EUR][1000 genomes]
rs4687614	1.00[JPT][hapmap]
rs4687617	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4687618	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4687619	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4687621	0.81[EUR][1000 genomes]
rs498778	1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs498946	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs575476	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61734640	0.81[EUR][1000 genomes]
rs634382	0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6414568	0.81[EUR][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445484	0.81[EUR][1000 genomes]
rs6445485	0.81[EUR][1000 genomes]
rs6445486	1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs6445506	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes]
rs66462821	0.92[ASN][1000 genomes]
rs676034	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6782162	0.81[EUR][1000 genomes]
rs6784615	0.82[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6787493	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6795333	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs71297391	0.81[EUR][1000 genomes]
rs71297394	0.81[EUR][1000 genomes]
rs71297395	0.81[EUR][1000 genomes]
rs71297396	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs728408	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs758800	0.81[EUR][1000 genomes]
rs758803	1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs7620015	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs82825	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs887514	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs887515	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs929528	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9844183	1.00[JPT][hapmap]
rs9846089	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9847332	0.81[EUR][1000 genomes]
rs9850471	0.81[EUR][1000 genomes]
rs9855470	1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs9861879	0.85[ASN][1000 genomes]
rs9863753	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9867823	1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52445600-52471600	Weak transcription	Gastric	stomach
2	chr3:52446400-52470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:52447000-52470200	Weak transcription	Fetal Lung	lung
4	chr3:52448600-52471200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:52450200-52478400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:52462800-52469200	Enhancers	Adipose Nuclei	Adipose
7	chr3:52462800-52469800	Enhancers	Placenta	Placenta
8	chr3:52462800-52473600	Enhancers	Fetal Muscle Leg	muscle
9	chr3:52463000-52469200	Enhancers	Fetal Muscle Trunk	muscle
10	chr3:52463000-52469200	Enhancers	Left Ventricle	heart
11	chr3:52463400-52470400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:52464600-52477400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:52465200-52469200	Enhancers	Right Atrium	heart
14	chr3:52465600-52469200	Enhancers	Right Ventricle	heart
15	chr3:52465600-52470800	Enhancers	Fetal Heart	heart
16	chr3:52466000-52469000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:52466000-52469600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:52466000-52471400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:52466400-52469400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:52466400-52473200	Enhancers	Spleen	Spleen
21	chr3:52467400-52477600	Weak transcription	HUVEC	blood vessel
22	chr3:52467600-52469000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:52467600-52469200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:52467600-52469200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:52467600-52469400	Enhancers	HMEC	breast
26	chr3:52467600-52472400	Enhancers	Lung	lung
27	chr3:52468000-52469000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr3:52468000-52470200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:52468000-52471600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:52468000-52472400	Weak transcription	HepG2	liver
31	chr3:52468200-52469200	Weak transcription	HSMMtube	muscle
32	chr3:52468200-52472000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:52468600-52469000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:52468600-52469200	Enhancers	Colonic Mucosa	Colon
35	chr3:52468600-52470000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:52468600-52470600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:52468600-52471800	Weak transcription	Pancreas	Pancrea
38	chr3:52468600-52477600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:52468800-52470400	Weak transcription	Ovary	ovary
40	chr3:52468800-52471400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:52468800-52471400	Weak transcription	NHEK	skin
42	chr3:52468800-52471600	Weak transcription	Esophagus	oesophagus

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