Variant report

Variant	rs12062561
Chromosome Location	chr1:180470739-180470740
allele	A/C
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180470530..180472800-chr1:181059348..181062070,2	MCF-7	breast:
2	chr1:180470531..180473320-chr1:180599332..180602016,2	K562	blood:
3	chr1:180469616..180471969-chr1:181074123..181075942,2	K562	blood:
4	chr1:180469285..180472037-chr1:180483861..180487907,3	K562	blood:
5	chr1:179922809..179925375-chr1:180469288..180472844,3	MCF-7	breast:
6	chr1:180470493..180473506-chr1:180597830..180602116,4	MCF-7	breast:
7	chr1:180438874..180441365-chr1:180469997..180471942,2	K562	blood:
8	chr1:180208860..180211195-chr1:180470402..180471972,2	MCF-7	breast:
9	chr1:180468948..180471810-chr1:180491211..180493029,2	MCF-7	breast:
10	chr1:180470101..180473441-chr1:181055955..181060608,7	K562	blood:
11	chr1:180139648..180141218-chr1:180469440..180471988,2	MCF-7	breast:
12	chr1:180167194..180169146-chr1:180469710..180471466,2	MCF-7	breast:
13	chr1:180470305..180472005-chr1:180744201..180746153,2	K562	blood:
14	chr1:180221964..180223660-chr1:180469973..180471619,2	MCF-7	breast:
15	chr1:180470474..180472036-chr1:181074031..181076331,2	K562	blood:
16	chr1:180197528..180200245-chr1:180468948..180472883,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction
ENSG00000162783	Chromatin interaction
ENSG00000272198	Chromatin interaction
ENSG00000121454	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10494528	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10494529	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913988	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913990	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913991	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913992	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913995	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913996	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10914004	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10914012	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11487431	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12058221	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065388	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12069389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12070624	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12071353	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12076995	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12077656	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12077791	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077839	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081494	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12083900	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12084039	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12087060	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12087325	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12089373	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12093073	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1339721	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16856042	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4403592	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55660948	0.83[EUR][1000 genomes]
rs55962675	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56303477	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56333717	0.83[EUR][1000 genomes]
rs56747078	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57070632	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57424497	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57493263	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58145394	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58369506	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59357483	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59371134	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60528279	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61024380	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425635	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6659477	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66619942	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6663823	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6667388	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6670242	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6673113	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6676778	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66913400	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6696075	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67071426	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67343454	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67517246	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67621570	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67623108	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67716213	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67830766	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68010689	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68046305	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72714872	0.83[EUR][1000 genomes]
rs72714883	0.83[EUR][1000 genomes]
rs72714890	0.83[EUR][1000 genomes]
rs72714891	0.83[EUR][1000 genomes]
rs72714892	0.83[EUR][1000 genomes]
rs72714894	0.83[EUR][1000 genomes]
rs72714896	0.83[EUR][1000 genomes]
rs72716605	0.83[EUR][1000 genomes]
rs72716619	0.88[EUR][1000 genomes]
rs72716624	0.88[EUR][1000 genomes]
rs72716634	0.90[EUR][1000 genomes]
rs72716637	0.93[EUR][1000 genomes]
rs72720921	0.83[EUR][1000 genomes]
rs73037411	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73048237	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7542223	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7552701	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
7	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180437600-180471000	Weak transcription	Lung	lung
2	chr1:180455600-180471000	Weak transcription	Left Ventricle	heart
3	chr1:180456000-180471000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:180458000-180471000	Weak transcription	Aorta	Aorta
5	chr1:180459200-180471000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:180468200-180471000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:180468200-180472600	Active TSS	GM12878-XiMat	blood
8	chr1:180468400-180470800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr1:180468400-180470800	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:180468600-180470800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:180468600-180471000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:180469400-180470800	Enhancers	Fetal Brain Male	brain
13	chr1:180469400-180470800	Enhancers	Thymus	Thymus
14	chr1:180469400-180471000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:180469600-180470800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:180469600-180471200	Flanking Active TSS	Dnd41	blood
17	chr1:180469800-180470800	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:180469800-180470800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr1:180469800-180470800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:180469800-180470800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:180469800-180471000	Enhancers	Colon Smooth Muscle	Colon
22	chr1:180469800-180471000	Flanking Active TSS	Hela-S3	cervix
23	chr1:180469800-180471200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:180470000-180470800	Enhancers	Primary B cells from cord blood	blood
25	chr1:180470000-180470800	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr1:180470000-180470800	Weak transcription	Ovary	ovary
27	chr1:180470000-180470800	Flanking Active TSS	NHEK	skin
28	chr1:180470000-180471000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:180470000-180471000	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:180470000-180471000	Weak transcription	Gastric	stomach
31	chr1:180470000-180471200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:180470000-180471400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:180470000-180471400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:180470000-180472200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:180470000-180472200	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr1:180470000-180472800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr1:180470200-180470800	Enhancers	Primary hematopoietic stem cells	blood
38	chr1:180470200-180470800	Enhancers	Fetal Stomach	stomach
39	chr1:180470200-180470800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr1:180470200-180470800	Flanking Active TSS	HepG2	liver
41	chr1:180470200-180471000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:180470200-180471000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:180470200-180471000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr1:180470200-180471000	Enhancers	Placenta Amnion	Placenta Amnion
45	chr1:180470200-180471000	Enhancers	Small Intestine	intestine
46	chr1:180470200-180471200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr1:180470200-180471200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:180470200-180471400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:180470200-180472200	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:180470200-180472200	Active TSS	iPS-20b Cell Line	embryonic stem cell

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