Variant report

Variant	rs1011064
Chromosome Location	chr3:52504503-52504504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52487939..52491238-chr3:52504089..52507877,6	MCF-7	breast:
2	chr3:52503525..52506168-chr3:52566167..52568849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114854	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1011062	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011063	1.00[JPT][hapmap]
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];0.91[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];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123598	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[JPT][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]
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];0.91[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	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109559	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[CEU][hapmap];1.00[JPT][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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs34827613	0.82[AMR][1000 genomes]
rs35860312	1.00[JPT][hapmap]
rs3755810	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[CEU][hapmap];1.00[JPT][hapmap];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];0.81[EUR][1000 genomes]
rs419050	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs419604	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs419752	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4312651	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687541	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687543	0.85[EUR][1000 genomes]
rs4687544	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687614	1.00[CEU][hapmap];1.00[JPT][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	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687618	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687621	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498778	1.00[JPT][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];0.81[EUR][1000 genomes]
rs634382	1.00[JPT][hapmap]
rs6414568	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[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	0.82[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782162	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];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[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs758800	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs758803	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929529	1.00[AFR][1000 genomes];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];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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[CEU][hapmap];1.00[JPT][hapmap];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	chr3:52491800-52506400	Weak transcription	Stomach Mucosa	stomach
4	chr3:52491800-52517200	Strong transcription	Fetal Stomach	stomach
5	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:52492000-52516800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:52492000-52517200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:52492200-52506200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:52492400-52517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:52493000-52506800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:52493200-52507000	Strong transcription	Fetal Thymus	thymus
16	chr3:52493400-52504800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:52493400-52505000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:52493400-52505800	Weak transcription	Psoas Muscle	Psoas
19	chr3:52493400-52506000	Weak transcription	Hela-S3	cervix
20	chr3:52493400-52506000	Weak transcription	K562	blood
21	chr3:52493400-52506400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:52495400-52504800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:52495400-52505000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:52495400-52507600	Weak transcription	Fetal Kidney	kidney
25	chr3:52495600-52505000	Weak transcription	Aorta	Aorta
26	chr3:52495600-52506200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:52496200-52504800	Weak transcription	Colonic Mucosa	Colon
28	chr3:52497400-52505600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:52498000-52506400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:52498600-52527200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:52499200-52505600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:52499200-52517200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:52499400-52527800	Strong transcription	Primary T cells from cord blood	blood
34	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr3:52499800-52504600	Weak transcription	Fetal Lung	lung
36	chr3:52499800-52505000	Weak transcription	Brain Angular Gyrus	brain
37	chr3:52499800-52507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:52500000-52504600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:52500000-52504800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:52500000-52505400	Weak transcription	A549	lung
41	chr3:52500200-52505000	Weak transcription	Primary B cells from cord blood	blood
42	chr3:52500200-52517000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:52500400-52504800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:52500800-52504600	Weak transcription	NH-A	brain
45	chr3:52500800-52504800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:52500800-52505000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:52501000-52504600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:52501000-52504600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:52501000-52504800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:52501000-52505000	Weak transcription	Rectal Smooth Muscle	rectum

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