Variant report

Variant	rs82825
Chromosome Location	chr3:52471942-52471943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52468984..52472313-chr3:52476961..52479325,3	K562	blood:
2	chr3:52463683..52467756-chr3:52469500..52473710,3	K562	blood:
3	chr3:52470597..52472566-chr3:52486223..52488356,2	K562	blood:
4	chr3:52471886..52474834-chr3:52476062..52479987,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010319	Chromatin interaction
ENSG00000114854	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1011064	1.00[JPT][hapmap]
rs1077142	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10865972	1.00[JPT][hapmap]
rs11705963	0.89[EUR][1000 genomes]
rs11706001	0.88[EUR][1000 genomes]
rs11706108	0.89[EUR][1000 genomes]
rs11707864	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs11707931	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11709658	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs11711934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11711974	0.84[YRI][hapmap]
rs11714402	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11716017	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes]
rs11718125	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[JPT][hapmap]
rs123602	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs123603	1.00[JPT][hapmap]
rs13059674	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13075370	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs17052058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs17052061	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17052068	0.92[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2016575	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2215466	1.00[JPT][hapmap]
rs2335640	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs28481563	0.89[EUR][1000 genomes]
rs2878549	1.00[JPT][hapmap]
rs34238085	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34261027	0.90[EUR][1000 genomes]
rs34355561	0.89[EUR][1000 genomes]
rs34523877	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34762015	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs34908451	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35133416	0.88[EUR][1000 genomes]
rs35860312	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs3752819	0.89[EUR][1000 genomes]
rs3774409	1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs390802	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs409803	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs419050	1.00[JPT][hapmap]
rs419604	1.00[JPT][hapmap]
rs419752	1.00[JPT][hapmap]
rs4312651	1.00[JPT][hapmap]
rs4687614	1.00[JPT][hapmap]
rs4687617	1.00[JPT][hapmap]
rs4687618	1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[JPT][hapmap]
rs498946	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55965068	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55997317	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56357549	0.88[EUR][1000 genomes]
rs57441156	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59612757	0.88[EUR][1000 genomes]
rs61150019	0.88[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs634382	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445386	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6445486	1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs66462821	0.88[EUR][1000 genomes]
rs67248391	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap]
rs6763882	0.92[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6794675	0.85[EUR][1000 genomes]
rs6796333	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6800707	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6810027	1.00[JPT][hapmap]
rs728408	1.00[JPT][hapmap]
rs758803	1.00[JPT][hapmap]
rs7620015	1.00[JPT][hapmap]
rs7643570	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs887514	1.00[JPT][hapmap]
rs887515	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs929528	1.00[JPT][hapmap]
rs9844183	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[JPT][hapmap]
rs9861879	0.89[EUR][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv590303	chr3:52469785-52478428	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52450200-52478400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:52462800-52473600	Enhancers	Fetal Muscle Leg	muscle
3	chr3:52464600-52477400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:52466400-52473200	Enhancers	Spleen	Spleen
5	chr3:52467400-52477600	Weak transcription	HUVEC	blood vessel
6	chr3:52467600-52472400	Enhancers	Lung	lung
7	chr3:52468000-52472400	Weak transcription	HepG2	liver
8	chr3:52468200-52472000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:52468600-52477600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:52469000-52478200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:52469200-52476800	Weak transcription	Left Ventricle	heart
12	chr3:52469600-52475200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:52470200-52472000	Enhancers	HSMMtube	muscle
14	chr3:52470400-52472000	Enhancers	Ovary	ovary
15	chr3:52470400-52475000	Genic enhancers	Adipose Nuclei	Adipose
16	chr3:52470800-52484200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:52471000-52472200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr3:52471000-52473600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:52471000-52475600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:52471200-52477200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:52471400-52472000	Bivalent Enhancer	Placenta	Placenta
22	chr3:52471400-52472400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:52471400-52472800	Enhancers	HMEC	breast
24	chr3:52471400-52473600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:52471400-52478000	Weak transcription	Right Atrium	heart
26	chr3:52471600-52472000	Genic enhancers	Right Ventricle	heart
27	chr3:52471600-52472200	Enhancers	Gastric	stomach
28	chr3:52471600-52472200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr3:52471600-52472600	Enhancers	Esophagus	oesophagus
30	chr3:52471600-52472600	Enhancers	Stomach Mucosa	stomach
31	chr3:52471600-52474200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:52471600-52475400	Weak transcription	Fetal Stomach	stomach
33	chr3:52471800-52472000	Enhancers	Pancreas	Pancrea
34	chr3:52471800-52472000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:52471800-52472000	Enhancers	Stomach Smooth Muscle	stomach
36	chr3:52471800-52472200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:52471800-52472200	Enhancers	Colonic Mucosa	Colon
38	chr3:52471800-52472200	Flanking Active TSS	NHEK	skin
39	chr3:52471800-52472400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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