Variant report

Variant	rs13076508
Chromosome Location	chr3:52407805-52407806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52272390..52274822-chr3:52406008..52407949,2	K562	blood:
2	chr3:52406156..52409184-chr3:52415561..52421026,5	K562	blood:
3	chr3:52321755..52323526-chr3:52405745..52408434,2	K562	blood:
4	chr3:52406883..52409184-chr3:52415694..52419355,3	K562	blood:

Variant related genes	Relation type
ENSG00000239732	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000168237	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[JPT][hapmap]
rs1035002	0.91[AMR][1000 genomes]
rs1077142	1.00[JPT][hapmap]
rs10865972	1.00[JPT][hapmap]
rs11706001	0.87[ASN][1000 genomes]
rs11707864	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11707931	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11709658	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11718125	1.00[JPT][hapmap]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065677	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13071708	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13074649	0.87[AMR][1000 genomes]
rs13075370	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13076890	1.00[JPT][hapmap]
rs13089892	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091360	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091545	1.00[JPT][hapmap]
rs13093555	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13096571	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098856	0.91[AMR][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164636	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs164637	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2016575	1.00[JPT][hapmap]
rs2109557	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs2335640	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2878549	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181173	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34332947	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34355561	1.00[ASN][1000 genomes]
rs34385735	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34628357	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762015	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34827613	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34908451	1.00[ASN][1000 genomes]
rs35130772	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35133416	1.00[ASN][1000 genomes]
rs352141	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	1.00[JPT][hapmap]
rs352144	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs352173	1.00[JPT][hapmap]
rs353545	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs353548	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs35860312	1.00[JPT][hapmap]
rs35982798	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752819	1.00[ASN][1000 genomes]
rs3755810	0.95[AMR][1000 genomes]
rs3774409	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796342	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3796343	1.00[JPT][hapmap]
rs390802	1.00[JPT][hapmap]
rs409803	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs419050	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419604	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419752	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312651	1.00[JPT][hapmap]
rs4687541	0.87[AMR][1000 genomes]
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];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498946	1.00[JPT][hapmap]
rs56357549	1.00[ASN][1000 genomes]
rs575476	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61150019	1.00[ASN][1000 genomes]
rs613519	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs61734640	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634382	1.00[JPT][hapmap]
rs6445386	1.00[JPT][hapmap]
rs6445486	1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs67248391	1.00[ASN][1000 genomes]
rs676034	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs6763882	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6771558	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs67834575	1.00[ASN][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6794675	1.00[ASN][1000 genomes]
rs6795333	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[JPT][hapmap]
rs71297391	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297394	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297395	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297396	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	1.00[JPT][hapmap]
rs758803	1.00[JPT][hapmap]
rs7620015	1.00[JPT][hapmap]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[JPT][hapmap]
rs887515	1.00[JPT][hapmap]
rs929528	1.00[JPT][hapmap]
rs9844183	1.00[JPT][hapmap]
rs9846089	1.00[JPT][hapmap]
rs9850471	0.87[AMR][1000 genomes]
rs9855470	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv979834	chr3:52407592-52408592	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
4	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
6	chr3:52395400-52409400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
8	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
10	chr3:52399000-52409400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:52399400-52409400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:52400200-52409200	Weak transcription	Right Ventricle	heart
13	chr3:52401000-52409400	Weak transcription	Esophagus	oesophagus
14	chr3:52401200-52409400	Weak transcription	Colonic Mucosa	Colon
15	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:52404800-52409200	Weak transcription	Pancreas	Pancrea
17	chr3:52405000-52408400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:52405000-52409200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:52405000-52409200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:52405000-52409400	Weak transcription	Brain Angular Gyrus	brain
21	chr3:52405000-52409400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
23	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:52405600-52409200	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:52405600-52409200	Weak transcription	Lung	lung
26	chr3:52406200-52409200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:52406200-52409400	Enhancers	GM12878-XiMat	blood
28	chr3:52406400-52408000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:52406400-52408000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:52406400-52408000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:52406400-52409400	Weak transcription	Brain Anterior Caudate	brain
32	chr3:52406400-52409400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:52406600-52408000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:52406600-52408000	Enhancers	Fetal Thymus	thymus
36	chr3:52406600-52409000	Weak transcription	Liver	Liver
37	chr3:52406600-52409200	Weak transcription	Placenta	Placenta
38	chr3:52406600-52409400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:52406600-52409400	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:52406600-52409400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:52406600-52409400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:52406800-52408000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr3:52406800-52409200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:52406800-52409200	Weak transcription	Fetal Stomach	stomach
45	chr3:52406800-52409400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:52407000-52408000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr3:52407000-52408400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:52407000-52409200	Weak transcription	Fetal Intestine Small	intestine
49	chr3:52407000-52409200	Weak transcription	Gastric	stomach
50	chr3:52407200-52409200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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