Variant report

Variant	rs6490076
Chromosome Location	chr12:116989212-116989213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:116717076..116718812-chr12:116987193..116990069,2	K562	blood:
2	chr12:116988969..116990503-chr12:117038058..117040021,2	K562	blood:
3	chr12:116986971..116990375-chr12:116994825..116997591,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP1LC3B2-1	chr12:116988920-116989617	XLOC_009898

Variant related genes	Relation type
ENSG00000171471	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10774871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10774872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10850662	0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10850663	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068062	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068070	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068072	0.86[AMR][1000 genomes]
rs11068075	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11609040	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11609872	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11610226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11615960	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1394801	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1394802	0.82[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2047952	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2089222	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2102294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2893685	0.90[ASN][1000 genomes]
rs60521218	0.95[ASN][1000 genomes]
rs6490075	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297552	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300418	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7304300	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315385	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954181	0.87[ASN][1000 genomes]
rs7961538	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7969190	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7969566	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7972701	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976256	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899540	chr12:116920503-116999861	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116978200-116989400	Weak transcription	Esophagus	oesophagus
2	chr12:116984200-116996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:116984200-116997000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:116986200-116989600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:116986600-116989600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:116986600-116990200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:116986600-116993000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:116986600-116993400	Weak transcription	Fetal Brain Male	brain
9	chr12:116986600-116994800	Weak transcription	Thymus	Thymus
10	chr12:116986800-116989400	Weak transcription	K562	blood
11	chr12:116986800-116989400	Weak transcription	NH-A	brain
12	chr12:116986800-116989600	Weak transcription	Right Ventricle	heart
13	chr12:116986800-116990000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:116986800-116990200	Weak transcription	Spleen	Spleen
15	chr12:116987000-116989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:116987000-116989600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:116987000-116991200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:116987600-116990800	ZNF genes & repeats	GM12878-XiMat	blood
19	chr12:116987600-116994400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:116988000-116990400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:116988400-116990200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:116988400-116990400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:116988800-116992800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:116989000-116991000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr12:116989200-116991600	Enhancers	Monocytes-CD14+_RO01746	blood

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