Variant report

Variant	rs12120789
Chromosome Location	chr1:62700296-62700297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1050334	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789107	0.80[EUR][1000 genomes]
rs10889309	0.99[ASN][1000 genomes]
rs10889310	0.87[ASN][1000 genomes]
rs10889313	0.99[ASN][1000 genomes]
rs10889315	0.97[ASN][1000 genomes]
rs11207941	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207942	0.93[ASN][1000 genomes]
rs11207943	0.99[ASN][1000 genomes]
rs11207944	0.99[ASN][1000 genomes]
rs11207945	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207946	0.99[ASN][1000 genomes]
rs11207947	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207948	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12030846	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12089897	0.99[ASN][1000 genomes]
rs12096118	0.86[ASN][1000 genomes]
rs12131947	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12138777	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144282	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067994	0.99[ASN][1000 genomes]
rs2457812	0.86[ASN][1000 genomes]
rs2481689	0.85[ASN][1000 genomes]
rs2666478	0.85[ASN][1000 genomes]
rs2774928	0.99[ASN][1000 genomes]
rs41289438	1.00[ASN][1000 genomes]
rs4322258	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55673263	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56318037	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59025845	0.81[EUR][1000 genomes]
rs61775734	1.00[ASN][1000 genomes]
rs61775736	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61775737	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660963	0.99[ASN][1000 genomes]
rs6664672	0.86[ASN][1000 genomes]
rs6671554	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6680953	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688986	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696307	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696486	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553446	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62693600-62700800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:62693600-62700800	Enhancers	Placenta	Placenta
3	chr1:62695800-62703400	Weak transcription	Adipose Nuclei	Adipose
4	chr1:62696600-62703600	Weak transcription	Fetal Stomach	stomach
5	chr1:62697000-62702800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:62697000-62703600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:62697000-62706600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:62697200-62700400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:62697200-62702800	Weak transcription	A549	lung
10	chr1:62697400-62700400	Weak transcription	HSMM	muscle
11	chr1:62697400-62701800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:62697400-62702400	Weak transcription	NH-A	brain
13	chr1:62697400-62703200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:62698000-62701000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr1:62698200-62704000	Enhancers	NHEK	skin
16	chr1:62698600-62701000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:62698600-62701200	Enhancers	HepG2	liver
18	chr1:62698600-62704400	Enhancers	Hela-S3	cervix
19	chr1:62698800-62701000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:62699000-62702800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:62699000-62706600	Weak transcription	Fetal Lung	lung
22	chr1:62699000-62706800	Weak transcription	Pancreas	Pancrea
23	chr1:62699200-62700600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:62699200-62703600	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:62699600-62701200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:62699800-62701000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:62699800-62701000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:62699800-62701600	Weak transcription	HSMMtube	muscle
29	chr1:62699800-62704200	Enhancers	HMEC	breast
30	chr1:62700000-62701800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:62700000-62702400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:62700000-62702800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:62700000-62704000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:62700200-62700600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:62700200-62701000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr1:62700200-62701000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:62700200-62701200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr1:62700200-62703400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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