Variant report

Variant	rs180416
Chromosome Location	chr12:47169518-47169519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46885590..46888355-chr12:47169213..47171245,2	MCF-7	breast:
2	chr12:47168903..47170642-chr12:47170948..47173007,2	MCF-7	breast:
3	chr12:47162883..47165298-chr12:47167955..47169605,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139209	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11183605	0.81[EUR][1000 genomes]
rs11183608	0.94[EUR][1000 genomes]
rs12307895	0.81[EUR][1000 genomes]
rs12311710	0.81[EUR][1000 genomes]
rs12316767	0.94[EUR][1000 genomes]
rs1468970	0.94[AMR][1000 genomes]
rs1468971	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1468972	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs180403	0.87[CHB][hapmap];0.90[AMR][1000 genomes]
rs180405	0.87[CHB][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs180407	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs180408	0.80[CHB][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs180410	0.83[CHB][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs180412	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs180415	0.84[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs180417	0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs180419	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs180420	0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs180421	0.91[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs180426	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180429	0.91[CHB][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs180430	0.91[CHB][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2080689	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2287471	0.94[EUR][1000 genomes]
rs2408623	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2430916	0.94[AMR][1000 genomes]
rs2430920	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2430921	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2465582	0.87[CHB][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2465584	0.87[CHB][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2465595	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2465614	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2543334	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2543335	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2715775	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2715783	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7316285	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv826361	chr12:47159545-47200894	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47157400-47172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:47161600-47173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:47164200-47187800	Genic enhancers	Liver	Liver
4	chr12:47164800-47169600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:47165200-47187200	Weak transcription	Fetal Kidney	kidney
6	chr12:47165600-47182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:47165800-47169600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:47167000-47173200	Enhancers	HepG2	liver
9	chr12:47168400-47177600	Weak transcription	NHLF	lung
10	chr12:47168400-47180800	Weak transcription	Pancreas	Pancrea
11	chr12:47169000-47173600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:47169000-47177600	Weak transcription	HSMMtube	muscle
13	chr12:47169200-47171800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:47169200-47175600	Strong transcription	HSMM	muscle
15	chr12:47169400-47169600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:47169400-47172000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:47169400-47180000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:47169400-47182200	Weak transcription	Psoas Muscle	Psoas
19	chr12:47169400-47185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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