Variant report

Variant	rs13060192
Chromosome Location	chr3:52378540-52378541
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	chr3:52336627..52339541-chr3:52378479..52380909,2	K562	blood:

Extended variants
information (count: 121 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1011062	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[JPT][hapmap]
rs1077142	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10865972	1.00[JPT][hapmap]
rs11706001	0.87[ASN][1000 genomes]
rs11707864	1.00[CHD][hapmap];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[CHD][hapmap];1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11718125	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13065677	0.86[AMR][1000 genomes]
rs13071708	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs13075370	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13076508	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076890	1.00[JPT][hapmap]
rs13089892	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091360	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091545	1.00[JPT][hapmap]
rs13093555	0.82[AMR][1000 genomes]
rs13096571	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164636	0.82[AMR][1000 genomes]
rs164637	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2016575	1.00[JPT][hapmap]
rs2109557	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2109558	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs2109559	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs2335640	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2878549	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs34181173	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34332947	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34355561	1.00[ASN][1000 genomes]
rs34385735	0.82[AMR][1000 genomes]
rs34551211	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs34628357	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762015	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34827613	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34908451	1.00[ASN][1000 genomes]
rs35130772	0.86[AMR][1000 genomes]
rs35133416	1.00[ASN][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	1.00[JPT][hapmap]
rs352144	1.00[JPT][hapmap]
rs352173	1.00[JPT][hapmap]
rs353545	0.82[AMR][1000 genomes]
rs353548	1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs35860312	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs35982798	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752819	1.00[ASN][1000 genomes]
rs3755810	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs3774409	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796342	0.86[AMR][1000 genomes]
rs3796343	1.00[JPT][hapmap]
rs390802	1.00[JPT][hapmap]
rs409803	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs419050	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419604	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs419752	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312651	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs4687614	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs4687617	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs4687618	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs498946	1.00[JPT][hapmap]
rs56357549	1.00[ASN][1000 genomes]
rs575476	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61150019	1.00[ASN][1000 genomes]
rs613519	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs61734640	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634382	1.00[JPT][hapmap]
rs6445386	1.00[JPT][hapmap]
rs6445486	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs6445506	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs67248391	1.00[ASN][1000 genomes]
rs676034	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs6763882	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	1.00[ASN][1000 genomes]
rs6784615	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs6794675	1.00[ASN][1000 genomes]
rs6795333	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs71297391	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297394	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297395	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297396	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs758800	1.00[ASW][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs758803	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs7620015	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs887515	1.00[JPT][hapmap]
rs929528	1.00[JPT][hapmap]
rs9844183	1.00[JPT][hapmap]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][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	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	esv3428292	chr3:52376212-52382310	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13060192	ITIH4	cis	multi-tissue	Pritchard
rs13060192	STAB1	cis	multi-tissue	Pritchard
rs13060192	FLJ12442	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:52352000-52379800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:52352200-52379000	Weak transcription	Colonic Mucosa	Colon
5	chr3:52352200-52382000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:52352200-52384600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:52352600-52379400	Weak transcription	Pancreas	Pancrea
8	chr3:52354400-52379800	Weak transcription	Esophagus	oesophagus
9	chr3:52354800-52384000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:52358400-52380400	Weak transcription	Ovary	ovary
11	chr3:52362800-52378600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:52364200-52383000	Weak transcription	Fetal Lung	lung
13	chr3:52364400-52379400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
15	chr3:52366400-52383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:52366600-52379400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:52366600-52386600	Weak transcription	Aorta	Aorta
18	chr3:52366800-52383000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:52367200-52378600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:52367200-52379600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:52367600-52384400	Weak transcription	Fetal Kidney	kidney
22	chr3:52368400-52378600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:52368400-52383000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:52368800-52380200	Weak transcription	Left Ventricle	heart
25	chr3:52368800-52380400	Weak transcription	Placenta	Placenta
26	chr3:52368800-52380400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr3:52370600-52379600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:52372000-52379200	Weak transcription	Primary B cells from cord blood	blood
29	chr3:52372000-52379600	Weak transcription	NHLF	lung
30	chr3:52372000-52380400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:52372200-52379600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:52372400-52378600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:52372600-52379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:52372600-52379600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:52373800-52396000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:52374000-52378600	Weak transcription	Brain Angular Gyrus	brain
37	chr3:52374000-52378600	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:52374000-52382200	Weak transcription	Brain Germinal Matrix	brain
39	chr3:52374000-52385400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:52374000-52386200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:52374000-52399000	Weak transcription	Stomach Mucosa	stomach
42	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
43	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:52374400-52378600	Weak transcription	Right Ventricle	heart
45	chr3:52375400-52405600	Strong transcription	Lung	lung
46	chr3:52375800-52378600	Weak transcription	Thymus	Thymus
47	chr3:52375800-52381000	Strong transcription	Fetal Stomach	stomach
48	chr3:52376200-52378600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:52376200-52379400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:52376400-52402000	Weak transcription	Placenta Amnion	Placenta Amnion

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