Variant report

Variant	rs13089892
Chromosome Location	chr3:52413670-52413671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52413424..52415334-chr3:52416038..52418225,2	K562	blood:
2	chr3:52413340..52415440-chr3:52417250..52419187,2	MCF-7	breast:
3	chr3:52410804..52413361-chr3:52413563..52417960,4	K562	blood:

Variant related genes	Relation type
ENSG00000114841	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1011062	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs1035002	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1077142	1.00[CHD][hapmap]
rs11706001	0.87[ASN][1000 genomes]
rs11707864	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11707931	1.00[ASN][1000 genomes]
rs11709658	1.00[ASN][1000 genomes]
rs11714402	1.00[CHD][hapmap]
rs11716017	1.00[ASN][1000 genomes]
rs11718125	1.00[CHD][hapmap]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123603	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060192	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]
rs13065677	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13071708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13074649	0.87[AMR][1000 genomes]
rs13075370	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs13076508	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091360	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093555	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13096571	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098856	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs164636	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs164637	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17052068	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2109557	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109558	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs2109559	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs2215466	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2335640	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2878549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34332947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34355561	1.00[ASN][1000 genomes]
rs34385735	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34551211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34628357	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762015	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs34827613	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34908451	1.00[ASN][1000 genomes]
rs35130772	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35133416	1.00[ASN][1000 genomes]
rs352141	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs352144	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs353545	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs353548	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs35860312	1.00[CHD][hapmap]
rs35982798	0.91[AMR][1000 genomes];0.97[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];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3774409	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs3796342	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs409803	0.82[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs419050	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419752	1.00[CHD][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312651	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs4687541	0.87[AMR][1000 genomes]
rs4687614	1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs4687617	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs4687618	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs498778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357549	1.00[ASN][1000 genomes]
rs575476	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61150019	1.00[ASN][1000 genomes]
rs613519	0.82[MEX][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61734640	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445486	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs6445506	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs67248391	1.00[ASN][1000 genomes]
rs676034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6763882	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs6771558	0.87[AMR][1000 genomes]
rs67834575	1.00[ASN][1000 genomes]
rs6784615	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs6794675	1.00[ASN][1000 genomes]
rs6795333	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810027	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs71297391	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297394	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297395	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297396	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs758800	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs758803	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7620015	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs887514	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs9850471	0.87[AMR][1000 genomes]
rs9855470	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs9867823	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]

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	nsv590302	chr3:52407933-52428988	Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv965168	chr3:52409425-52416848	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 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	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
3	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
5	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
6	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
8	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
9	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
10	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:52407200-52413800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:52407200-52422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:52407600-52413800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:52407600-52420800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:52407800-52421600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:52408000-52419200	Weak transcription	Fetal Thymus	thymus
18	chr3:52408000-52421800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:52408000-52433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
21	chr3:52408600-52421000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:52408800-52414000	Weak transcription	K562	blood
23	chr3:52409600-52416000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:52409800-52418800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:52409800-52425200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:52410000-52425200	Weak transcription	Primary B cells from cord blood	blood
27	chr3:52410000-52433200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:52410000-52434400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:52410200-52416400	Weak transcription	Esophagus	oesophagus
30	chr3:52410200-52418800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:52410200-52420400	Weak transcription	Colonic Mucosa	Colon
32	chr3:52410200-52425000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:52410200-52426800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:52410400-52417400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:52410400-52417800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:52410400-52418000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr3:52410400-52418600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:52410400-52419000	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:52410400-52419200	Weak transcription	Brain Angular Gyrus	brain
40	chr3:52410400-52419400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:52410400-52420400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:52410600-52419000	Weak transcription	Adipose Nuclei	Adipose
43	chr3:52410600-52419200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:52410600-52419200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:52410600-52420200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:52410600-52420200	Weak transcription	Fetal Intestine Large	intestine
47	chr3:52410600-52422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:52410600-52424800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:52410600-52425000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:52410600-52435400	Weak transcription	Primary hematopoietic stem cells	blood

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