Variant report

Variant	rs1011062
Chromosome Location	chr3:52506903-52506904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52505487..52507011-chr3:52517843..52519757,2	K562	blood:
2	chr3:52506547..52508597-chr3:52570187..52573037,2	MCF-7	breast:
3	chr3:52487939..52491238-chr3:52504089..52507877,6	MCF-7	breast:
4	chr3:52505024..52507887-chr3:52527744..52529874,2	MCF-7	breast:
5	chr3:52488681..52492997-chr3:52505692..52511376,6	K562	blood:
6	chr3:52505027..52507504-chr3:52738535..52741338,2	MCF-7	breast:
7	chr3:52504996..52506918-chr3:52535565..52538055,2	MCF-7	breast:
8	chr3:52504515..52506973-chr3:52565446..52568302,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000114902	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000168268	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035002	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1035003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077142	1.00[JPT][hapmap]
rs10865972	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap]
rs11721286	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123598	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];0.83[EUR][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs13071708	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs13074649	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[JPT][hapmap]
rs13089892	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[JPT][hapmap]
rs13096571	0.80[EUR][1000 genomes]
rs1541495	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	1.00[JPT][hapmap]
rs2109557	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109558	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109559	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335640	1.00[JPT][hapmap]
rs2335928	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs34827613	0.82[AMR][1000 genomes]
rs35860312	1.00[JPT][hapmap]
rs3755810	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796343	1.00[JPT][hapmap]
rs390802	1.00[JPT][hapmap]
rs409803	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs419050	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs419604	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];0.88[EUR][1000 genomes]
rs419752	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]
rs4312651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687541	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687543	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4687544	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687545	1.00[AFR][1000 genomes]
rs4687614	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687616	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687617	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687621	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498778	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs498946	1.00[JPT][hapmap]
rs575476	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs634382	1.00[JPT][hapmap]
rs6414568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445483	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs676034	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787493	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795333	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs758800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs758802	1.00[AFR][1000 genomes]
rs758803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs887515	1.00[JPT][hapmap]
rs929528	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929529	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844183	1.00[JPT][hapmap]
rs9846089	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850471	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
4	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
5	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
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52491600-52509400	Weak transcription	Small Intestine	intestine
2	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
3	chr3:52491800-52517200	Strong transcription	Fetal Stomach	stomach
4	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:52492000-52516800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:52492000-52517200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:52492400-52517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:52493200-52507000	Strong transcription	Fetal Thymus	thymus
13	chr3:52495400-52507600	Weak transcription	Fetal Kidney	kidney
14	chr3:52498600-52527200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:52499200-52517200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:52499400-52527800	Strong transcription	Primary T cells from cord blood	blood
17	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:52499800-52507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:52500200-52517000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:52501000-52515200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
22	chr3:52502800-52517200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:52503400-52517200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:52503600-52507600	Weak transcription	Fetal Brain Male	brain
25	chr3:52504200-52517200	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr3:52504200-52526600	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr3:52504200-52526800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:52504200-52527400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:52504200-52527400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:52504200-52527600	Strong transcription	Dnd41	blood
31	chr3:52504200-52527800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:52504200-52528000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr3:52504200-52528000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:52504200-52528600	Strong transcription	Brain Germinal Matrix	brain
35	chr3:52504400-52508200	Strong transcription	NHLF	lung
36	chr3:52504400-52508400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:52504400-52517000	Strong transcription	GM12878-XiMat	blood
38	chr3:52504400-52517400	Strong transcription	NHEK	skin
39	chr3:52504400-52517600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:52504400-52523600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:52504400-52523800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:52504400-52527400	Strong transcription	Osteobl	bone
43	chr3:52504400-52527600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:52504400-52527600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:52504400-52528000	Strong transcription	Fetal Brain Female	brain
46	chr3:52504600-52515800	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:52504600-52517000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:52504600-52517000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:52504600-52517000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr3:52504600-52517000	Strong transcription	HSMMtube	muscle

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