Variant report

Variant	rs12408243
Chromosome Location	chr1:46990044-46990045
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46985914..46991197-chr1:46993744..46997835,5	K562	blood:
2	chr1:46985009..46990560-chr1:46990823..46993646,5	K562	blood:
3	chr1:46986798..46990832-chr1:46991693..46995331,8	K562	blood:
4	chr1:46950640..46959255-chr1:46986389..46991936,15	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11211301	0.83[AMR][1000 genomes]
rs12059461	1.00[JPT][hapmap]
rs1258045	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12736095	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1317949	0.81[EUR][1000 genomes]
rs2404609	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2486166	0.82[MEX][hapmap]
rs33998070	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35051406	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs956527	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1010578	chr1:46977818-47010579	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12408243	TESK2	cis	cerebellum	SCAN
rs12408243	ERMAP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46985000-46990200	Enhancers	HMEC	breast
2	chr1:46986600-46991200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:46987200-46990600	Enhancers	Esophagus	oesophagus
4	chr1:46987400-46990200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:46987600-46990400	Enhancers	Stomach Mucosa	stomach
6	chr1:46987800-46991000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr1:46987800-46993800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:46988400-46992400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:46988400-46992600	Weak transcription	Spleen	Spleen
10	chr1:46988600-46990200	Enhancers	NHEK	skin
11	chr1:46988600-46990400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:46988800-46990200	Enhancers	Hela-S3	cervix
13	chr1:46988800-46991000	Weak transcription	NH-A	brain
14	chr1:46988800-46998600	Weak transcription	Right Ventricle	heart
15	chr1:46989000-46993200	Weak transcription	Pancreas	Pancrea
16	chr1:46989000-46999000	Weak transcription	Gastric	stomach
17	chr1:46989200-46998600	Weak transcription	Right Atrium	heart
18	chr1:46989400-46990800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:46989400-46992600	Weak transcription	A549	lung
20	chr1:46989600-46991000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:46989800-46990800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr1:46989800-46994200	Enhancers	K562	blood
23	chr1:46990000-46990200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr1:46990000-46993800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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