Variant report

Variant	rs1491960
Chromosome Location	chr3:46120380-46120381
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:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:45874102..45874933-chr3:46120010..46120588,2	MCF-7	breast:
2	chr3:45978817..45979385-chr3:46120279..46120902,2	K562	blood:
3	chr3:45965432..45966076-chr3:46120033..46120908,2	K562	blood:
4	chr3:46120227..46120919-chr3:46249276..46249992,2	K562	blood:
5	chr3:46068989..46069803-chr3:46120051..46120552,2	K562	blood:
6	chr3:45970536..45971214-chr3:46120157..46120881,2	MCF-7	breast:
7	chr3:45881509..45882298-chr3:46120089..46120945,2	MCF-7	breast:
8	chr3:45987551..45988458-chr3:46119930..46120914,4	MCF-7	breast:
9	chr3:45874039..45874833-chr3:46120082..46121076,3	MCF-7	breast:
10	chr3:46119918..46120790-chr3:46468852..46469539,2	K562	blood:
11	chr11:64122644..64123473-chr3:46119922..46120607,2	MCF-7	breast:
12	chr3:45801846..45803268-chr3:46119981..46120996,10	K562	blood:
13	chr3:45970362..45970959-chr3:46120109..46120778,2	MCF-7	breast:
14	chr3:45978760..45981889-chr3:46119716..46121321,25	MCF-7	breast:
15	chr3:45970248..45970774-chr3:46120086..46120929,2	K562	blood:
16	chr3:45971111..45971673-chr3:46120113..46120665,2	MCF-7	breast:
17	chr3:46120043..46120896-chr3:46249782..46250471,4	MCF-7	breast:
18	chr3:45816597..45817280-chr3:46120013..46120834,2	K562	blood:
19	chr3:45978672..45979831-chr3:46120014..46120974,3	MCF-7	breast:
20	chr3:45078980..45079910-chr3:46120092..46120914,3	K562	blood:
21	chr3:45979895..45980974-chr3:46119979..46120805,8	MCF-7	breast:
22	chr3:45267642..45268312-chr3:46119980..46120949,2	K562	blood:
23	chr3:46103249..46106082-chr3:46119956..46121890,2	K562	blood:
24	chr3:45979945..45981160-chr3:46119722..46121315,21	K562	blood:

No data

Variant related genes	Relation type
ENSG00000168071	Chromatin interaction
ENSG00000163823	Chromatin interaction
ENSG00000173578	Chromatin interaction
ENSG00000249992	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10510747	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1118021	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12054287	0.89[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs12485978	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs12486449	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320534	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs13434141	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434336	0.96[AFR][1000 genomes]
rs1388602	0.81[ASN][1000 genomes]
rs1491959	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1546077	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1546079	0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1602580	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1604068	0.91[ASN][1000 genomes]
rs17078567	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17078589	0.98[ASN][1000 genomes]
rs2036295	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2173639	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2888512	0.97[ASN][1000 genomes]
rs3796376	0.89[CEU][hapmap]
rs4339141	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4447807	0.84[EUR][1000 genomes]
rs4490402	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4586860	0.97[ASN][1000 genomes]
rs4682804	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682805	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4682807	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4682810	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs4683169	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4683174	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56800498	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58035200	0.87[EUR][1000 genomes]
rs58260031	0.89[EUR][1000 genomes]
rs59865404	0.91[EUR][1000 genomes]
rs60539039	0.88[EUR][1000 genomes]
rs60991632	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61066315	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61254379	0.93[EUR][1000 genomes]
rs61387489	0.96[ASN][1000 genomes]
rs62242832	0.84[EUR][1000 genomes]
rs62242846	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62243869	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62243873	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62243875	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62243876	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62243906	0.83[EUR][1000 genomes]
rs6778958	0.97[ASN][1000 genomes]
rs6795629	0.81[JPT][hapmap]
rs6807854	0.85[EUR][1000 genomes]
rs751625	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623476	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs7641151	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7641164	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643426	0.84[CEU][hapmap]
rs880160	0.97[ASN][1000 genomes]
rs9818635	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849715	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9856805	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9990060	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46119800-46120400	Enhancers	Fetal Muscle Leg	muscle
2	chr3:46119800-46120800	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr3:46119800-46120800	Enhancers	HSMMtube	muscle
4	chr3:46119800-46121000	Enhancers	Dnd41	blood
5	chr3:46120000-46120400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:46120000-46120400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:46120000-46120400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr3:46120000-46120400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:46120000-46120400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:46120000-46120400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:46120000-46120400	Enhancers	Adipose Nuclei	Adipose
12	chr3:46120000-46120400	Enhancers	Ovary	ovary
13	chr3:46120000-46120400	Enhancers	Thymus	Thymus
14	chr3:46120000-46120400	Flanking Active TSS	HSMM	muscle
15	chr3:46120000-46120400	Active TSS	NHDF-Ad	bronchial
16	chr3:46120000-46120600	Enhancers	Primary T cells from cord blood	blood
17	chr3:46120000-46120600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr3:46120000-46120600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr3:46120000-46120600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:46120000-46120600	Enhancers	Fetal Stomach	stomach
21	chr3:46120000-46120800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:46120000-46120800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr3:46120000-46120800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:46120000-46121400	Enhancers	Fetal Thymus	thymus
25	chr3:46120000-46122400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:46120000-46122400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:46120000-46124000	Enhancers	Fetal Lung	lung
28	chr3:46120200-46120400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr3:46120200-46120400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:46120200-46120400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:46120200-46120400	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:46120200-46120400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr3:46120200-46120400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:46120200-46120400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
35	chr3:46120200-46120400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:46120200-46120400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:46120200-46120400	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr3:46120200-46120400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:46120200-46120400	Enhancers	Fetal Heart	heart
40	chr3:46120200-46120400	Enhancers	GM12878-XiMat	blood
41	chr3:46120200-46120400	Enhancers	HMEC	breast
42	chr3:46120200-46120400	Flanking Bivalent TSS/Enh	K562	blood
43	chr3:46120200-46120400	Enhancers	NHEK	skin
44	chr3:46120200-46120400	Flanking Active TSS	Osteobl	bone
45	chr3:46120200-46120600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr3:46120200-46120600	Active TSS	Primary B cells from cord blood	blood
47	chr3:46120200-46120600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:46120200-46120600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:46120200-46120600	Enhancers	Duodenum Mucosa	Duodenum
50	chr3:46120200-46120600	Active TSS	Fetal Brain Male	brain

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