Variant report

Variant	rs41289438
Chromosome Location	chr1:62704134-62704135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1050334	1.00[ASN][1000 genomes]
rs10889302	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10889303	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10889305	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10889309	0.99[ASN][1000 genomes]
rs10889310	0.87[ASN][1000 genomes]
rs10889313	0.99[ASN][1000 genomes]
rs10889315	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207938	0.81[AMR][1000 genomes]
rs11207941	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207942	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207943	0.99[ASN][1000 genomes]
rs11207944	0.99[ASN][1000 genomes]
rs11207945	0.99[ASN][1000 genomes]
rs11207946	0.99[ASN][1000 genomes]
rs11207947	0.88[ASN][1000 genomes]
rs11207948	0.87[ASN][1000 genomes]
rs12030846	0.93[ASN][1000 genomes]
rs12040080	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12043306	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12048000	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12089897	0.99[ASN][1000 genomes]
rs12096118	0.86[ASN][1000 genomes]
rs12120789	1.00[ASN][1000 genomes]
rs12133752	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12138777	0.96[ASN][1000 genomes]
rs12144282	1.00[ASN][1000 genomes]
rs12144690	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2067994	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2365990	0.84[AMR][1000 genomes];0.89[EUR][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]
rs28562952	0.81[EUR][1000 genomes]
rs4019803	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4322258	0.91[ASN][1000 genomes]
rs55673263	0.87[ASN][1000 genomes]
rs55675042	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55831250	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56318037	0.86[ASN][1000 genomes]
rs61775734	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61775736	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61775737	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660963	0.99[ASN][1000 genomes]
rs6664672	0.86[ASN][1000 genomes]
rs6669211	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6680953	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688986	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696307	0.99[ASN][1000 genomes]
rs6696486	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72679772	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72679773	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72679787	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72679795	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72679796	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7411110	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7516473	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7528199	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7538818	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7539028	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7541340	0.84[AMR][1000 genomes];0.89[EUR][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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62697000-62706600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:62698600-62704400	Enhancers	Hela-S3	cervix
3	chr1:62699000-62706600	Weak transcription	Fetal Lung	lung
4	chr1:62699000-62706800	Weak transcription	Pancreas	Pancrea
5	chr1:62699800-62704200	Enhancers	HMEC	breast
6	chr1:62701000-62707400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:62701000-62710800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:62701400-62709400	Weak transcription	Fetal Intestine Small	intestine
9	chr1:62701600-62704200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:62701600-62704200	Enhancers	HSMMtube	muscle
11	chr1:62701600-62705000	Enhancers	HepG2	liver
12	chr1:62702000-62704200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:62702200-62706800	Weak transcription	Liver	Liver
14	chr1:62702800-62704200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:62702800-62704400	Enhancers	A549	lung
16	chr1:62703200-62704200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:62703200-62704400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:62703400-62704200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr1:62703400-62704200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:62703400-62704200	Strong transcription	Adipose Nuclei	Adipose
21	chr1:62703400-62704200	Enhancers	Placenta	Placenta
22	chr1:62703400-62704400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:62703600-62704200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:62703600-62704200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr1:62703600-62704200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:62703600-62704200	Genic enhancers	Fetal Muscle Leg	muscle
27	chr1:62703600-62704600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:62703800-62704200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:62703800-62704400	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr1:62703800-62707000	Weak transcription	Fetal Kidney	kidney
31	chr1:62704000-62704200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:62704000-62704400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:62704000-62704400	Strong transcription	Fetal Stomach	stomach
34	chr1:62704000-62706400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:62704000-62706600	Weak transcription	Fetal Heart	heart
36	chr1:62704000-62706600	Weak transcription	HSMM	muscle
37	chr1:62704000-62710600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:62704000-62711400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:62704000-62720600	Weak transcription	Right Atrium	heart

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