Variant report

Variant	rs12403980
Chromosome Location	chr1:239852943-239852944
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1014670	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10737838	0.84[AMR][1000 genomes]
rs10802793	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10925956	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1155612	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12406493	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12407154	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12751235	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1431718	0.87[ASN][1000 genomes]
rs1431719	0.81[AFR][1000 genomes]
rs1431721	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2217532	0.83[AFR][1000 genomes]
rs2278642	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2278643	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2278644	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2355210	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2355237	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2355238	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2883621	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738436	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs56266008	0.87[ASN][1000 genomes]
rs61834818	0.80[ASN][1000 genomes]
rs6429152	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6429153	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6429154	0.80[AFR][1000 genomes]
rs6657343	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6688537	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6688548	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6694220	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6695600	0.81[AFR][1000 genomes]
rs714266	0.87[ASN][1000 genomes]
rs717227	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7511970	0.82[AFR][1000 genomes]
rs7551919	0.89[ASN][1000 genomes]
rs7552453	0.82[AMR][1000 genomes]
rs891700	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs961065	0.87[ASN][1000 genomes]
rs988231	0.89[EUR][1000 genomes];0.93[ASN][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	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2757778	chr1:239766094-240389504	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv2759009	chr1:239766094-240389504	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv3440138	chr1:239850754-239853302	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3349682	chr1:239850929-239853177	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239836600-239856200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:239840000-239853200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:239841000-239854000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:239845000-239855200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:239845000-239879800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:239849800-239856600	Weak transcription	Fetal Intestine Small	intestine
7	chr1:239852600-239853200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:239852600-239853200	Active TSS	Ovary	ovary
9	chr1:239852800-239853200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr1:239852800-239853200	Active TSS	Fetal Lung	lung
11	chr1:239852800-239853200	Active TSS	A549	lung

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