Variant report

Variant	rs419050
Chromosome Location	chr3:52426884-52426885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52420539..52424070-chr3:52425084..52430819,9	K562	blood:
2	chr3:52425590..52427508-chr3:52428008..52430863,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114841	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1011062	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1035002	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1035003	0.82[AMR][1000 genomes]
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[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	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]
rs13065677	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13071708	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13074649	0.91[AMR][1000 genomes]
rs13075370	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13076508	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076890	1.00[JPT][hapmap]
rs13089892	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]
rs13091360	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091545	1.00[JPT][hapmap]
rs13093555	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13096571	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098856	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164636	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs164637	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][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	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109558	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2109559	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2335640	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2335928	0.82[AMR][1000 genomes]
rs2335929	0.82[AMR][1000 genomes]
rs2878549	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181173	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34332947	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34355561	1.00[ASN][1000 genomes]
rs34385735	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34551211	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34628357	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762015	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34827613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34908451	1.00[ASN][1000 genomes]
rs35130772	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35133416	1.00[ASN][1000 genomes]
rs352141	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	1.00[JPT][hapmap]
rs352144	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs352173	1.00[JPT][hapmap]
rs353545	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs353548	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs35860312	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs35982798	0.86[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];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3774409	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796342	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3796343	1.00[JPT][hapmap]
rs390802	1.00[JPT][hapmap]
rs409803	1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs419604	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419752	1.00[ASW][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312651	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]
rs4687541	0.91[AMR][1000 genomes]
rs4687614	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs4687617	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs4687618	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498946	1.00[JPT][hapmap]
rs56357549	1.00[ASN][1000 genomes]
rs575476	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61150019	1.00[ASN][1000 genomes]
rs613519	1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61734640	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634382	1.00[JPT][hapmap]
rs6414568	0.82[AMR][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445484	0.82[AMR][1000 genomes]
rs6445485	0.82[AMR][1000 genomes]
rs6445486	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]
rs6445506	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs67248391	1.00[ASN][1000 genomes]
rs676034	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6763882	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6771558	1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs6782162	0.82[AMR][1000 genomes]
rs67834575	1.00[ASN][1000 genomes]
rs6784615	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs6794675	1.00[ASN][1000 genomes]
rs6795333	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs71297391	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297394	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297395	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297396	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs758800	1.00[GIH][hapmap];0.92[TSI][hapmap]
rs758803	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7620015	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs887515	1.00[JPT][hapmap]
rs929528	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs929529	0.82[AMR][1000 genomes]
rs9844183	1.00[JPT][hapmap]
rs9846089	1.00[JPT][hapmap]
rs9847332	0.82[AMR][1000 genomes]
rs9850471	0.91[AMR][1000 genomes]
rs9855470	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[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	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

No data

Chromatin state (count:85 , 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	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:52408000-52433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
10	chr3:52410000-52433200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:52410000-52434400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:52410600-52435400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:52413800-52433000	Weak transcription	Fetal Brain Female	brain
14	chr3:52414000-52433200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:52414000-52435400	Weak transcription	Fetal Lung	lung
16	chr3:52414800-52434800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:52418600-52442200	Strong transcription	Fetal Intestine Small	intestine
18	chr3:52418800-52430000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:52418800-52430000	Strong transcription	Brain Cingulate Gyrus	brain
20	chr3:52418800-52430600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:52418800-52441800	Strong transcription	Brain Anterior Caudate	brain
22	chr3:52419000-52431200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:52419000-52441800	Strong transcription	Liver	Liver
24	chr3:52419000-52442000	Strong transcription	Brain Hippocampus Middle	brain
25	chr3:52419000-52442600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:52419200-52429800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:52419200-52435400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:52419200-52441600	Strong transcription	Fetal Stomach	stomach
29	chr3:52419200-52441800	Strong transcription	Brain Angular Gyrus	brain
30	chr3:52419200-52442000	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr3:52419400-52428800	Strong transcription	Primary T cells from cord blood	blood
32	chr3:52419600-52432800	Weak transcription	Fetal Thymus	thymus
33	chr3:52419600-52435600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:52419800-52428000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:52420000-52442000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:52420200-52442600	Strong transcription	Fetal Intestine Large	intestine
39	chr3:52420400-52428200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:52420400-52428400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:52421400-52428200	Strong transcription	Brain Substantia Nigra	brain
42	chr3:52422200-52428200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:52422200-52428800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:52422600-52441800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:52423600-52434200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:52424400-52428200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:52424400-52428400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr3:52424400-52428400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr3:52424400-52430000	Strong transcription	Placenta	Placenta
50	chr3:52424600-52427000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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