Variant report

Variant	rs7488577
Chromosome Location	chr12:46866955-46866956
allele	A/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46763709..46766577-chr12:46865824..46870117,4	K562	blood:
2	chr12:46766147..46767009-chr12:46866901..46867780,2	MCF-7	breast:
3	chr12:46857526..46859603-chr12:46866422..46869181,2	MCF-7	breast:
4	chr12:46862072..46864676-chr12:46865439..46867529,2	K562	blood:
5	chr12:46862072..46864676-chr12:46865439..46867529,3	K562	blood:
6	chr12:46774448..46777303-chr12:46865310..46867356,2	MCF-7	breast:
7	chr12:46760933..46763771-chr12:46865158..46867370,2	MCF-7	breast:
8	chr12:46662160..46665027-chr12:46865481..46867749,2	MCF-7	breast:
9	chr12:46848032..46851885-chr12:46865278..46868911,4	MCF-7	breast:
10	chr12:46865500..46867657-chr12:46876148..46878526,2	MCF-7	breast:
11	chr12:46865786..46868659-chr12:46883028..46885506,2	MCF-7	breast:
12	chr12:46764487..46767688-chr12:46865633..46870599,8	MCF-7	breast:
13	chr12:46865908..46869326-chr12:46872874..46876694,4	MCF-7	breast:
14	chr12:46772190..46774754-chr12:46865933..46867665,2	MCF-7	breast:
15	chr12:46865906..46867668-chr12:46868121..46870564,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10748450	0.88[AMR][1000 genomes]
rs10785628	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10785629	0.88[AMR][1000 genomes]
rs10880969	0.88[JPT][hapmap]
rs10880973	0.88[AMR][1000 genomes]
rs10880974	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183456	0.90[CHB][hapmap]
rs11183478	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11183479	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11183483	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11183502	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11183503	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11183504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1125909	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs11837427	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12313929	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12827740	0.82[AMR][1000 genomes]
rs1472178	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2131371	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2252238	0.95[CEU][hapmap]
rs3925101	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3936214	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4077707	0.92[AMR][1000 genomes]
rs4077708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4258438	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4427617	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4768123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4768709	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4768716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4768724	0.88[AMR][1000 genomes]
rs4768725	0.88[AMR][1000 genomes]
rs4768726	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768727	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768728	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768729	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768730	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768733	0.95[CEU][hapmap]
rs6582657	0.88[AMR][1000 genomes]
rs6582658	0.88[AMR][1000 genomes]
rs6582659	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582660	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6582661	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6582663	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7485599	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7486915	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7488144	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7954645	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7956314	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7960808	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7964767	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7980455	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9706162	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9706460	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9706520	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][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	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:46853200-46867400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:46856000-46867800	Weak transcription	Aorta	Aorta
4	chr12:46856200-46868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:46856600-46867400	Weak transcription	Placenta	Placenta
6	chr12:46858800-46867400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:46860200-46867400	Enhancers	Hela-S3	cervix
8	chr12:46861200-46867000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:46863200-46867400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:46863400-46867400	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:46863800-46867000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:46863800-46867200	Enhancers	Duodenum Mucosa	Duodenum
13	chr12:46863800-46867400	Enhancers	Fetal Lung	lung
14	chr12:46863800-46867600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:46863800-46867600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:46864000-46867600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:46864000-46867600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:46864000-46867600	Enhancers	NHDF-Ad	bronchial
19	chr12:46864000-46868600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:46864200-46867400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:46864200-46867600	Weak transcription	Thymus	Thymus
22	chr12:46864200-46867800	Enhancers	NHLF	lung
23	chr12:46864200-46877400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:46864400-46867200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:46864400-46867200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:46864400-46867400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:46864400-46867400	Weak transcription	Fetal Thymus	thymus
28	chr12:46864400-46867600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:46864400-46877400	Weak transcription	Primary T cells from cord blood	blood
30	chr12:46864800-46867200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:46864800-46867200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:46864800-46867400	Enhancers	NHEK	skin
33	chr12:46864800-46867600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr12:46864800-46867600	Enhancers	HSMM	muscle
35	chr12:46864800-46867600	Enhancers	Osteobl	bone
36	chr12:46864800-46868600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:46864800-46868600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:46864800-46868600	Enhancers	Stomach Mucosa	stomach
39	chr12:46864800-46868600	Enhancers	HMEC	breast
40	chr12:46864800-46868800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr12:46865000-46867000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:46865000-46867200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:46865000-46868200	Weak transcription	Spleen	Spleen
44	chr12:46865200-46867400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:46865200-46867400	Enhancers	NH-A	brain
46	chr12:46865200-46867600	Weak transcription	Small Intestine	intestine
47	chr12:46865400-46870200	Weak transcription	Lung	lung
48	chr12:46865400-46879200	Weak transcription	Right Ventricle	heart
49	chr12:46865600-46868800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:46865800-46867400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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