Variant report

Variant	rs60291089
Chromosome Location	chr2:74344890-74344891
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12619982	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2421752	0.86[ASN][1000 genomes]
rs4429500	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4452177	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4563249	0.85[EUR][1000 genomes]
rs56199245	0.84[ASN][1000 genomes]
rs58759652	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59570457	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60330274	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60705299	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60964317	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61521879	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6707619	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6707729	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715351	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6731793	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6737314	0.84[ASN][1000 genomes]
rs72911122	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72915068	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7571083	0.86[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	nsv874284	chr2:74283728-74348797	Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv874285	chr2:74283728-74355244	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs60291089	MGC10955	cis	Stomach	GTEx
rs60291089	MGC10955	cis	Artery Aorta	GTEx
rs60291089	FNBP1P1	cis	Muscle Skeletal	GTEx
rs60291089	MGC10955	cis	Adipose Subcutaneous	GTEx
rs60291089	FNBP1P1	cis	Stomach	GTEx
rs60291089	FNBP1P1	cis	Thyroid	GTEx
rs60291089	MGC10955	cis	Artery Tibial	GTEx
rs60291089	FNBP1P1	cis	lung	GTEx
rs60291089	MGC10955	cis	lung	GTEx
rs60291089	MGC10955	cis	Whole Blood	GTEx
rs60291089	FNBP1P1	cis	Artery Tibial	GTEx
rs60291089	MGC10955	cis	Skin Sun Exposed Lower leg	GTEx
rs60291089	FNBP1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs60291089	FNBP1P1	cis	Esophagus Mucosa	GTEx
rs60291089	FNBP1P1	cis	Esophagus Muscularis	GTEx
rs60291089	MGC10955	cis	Esophagus Mucosa	GTEx
rs60291089	MGC10955	cis	Nerve Tibial	GTEx
rs60291089	MGC10955	cis	Thyroid	GTEx
rs60291089	MGC10955	cis	Esophagus Muscularis	GTEx
rs60291089	FNBP1P1	cis	Artery Aorta	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74322200-74346600	Weak transcription	Hela-S3	cervix
2	chr2:74329600-74347000	Weak transcription	HSMMtube	muscle
3	chr2:74330200-74347000	Weak transcription	Aorta	Aorta
4	chr2:74330400-74346800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:74330600-74346600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:74330600-74347000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:74330600-74347000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:74330600-74347000	Weak transcription	Pancreas	Pancrea
9	chr2:74330800-74346800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:74330800-74347000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:74331200-74347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:74332000-74346400	Weak transcription	Dnd41	blood
13	chr2:74332000-74346800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:74332600-74346400	Weak transcription	GM12878-XiMat	blood
15	chr2:74332600-74347000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:74332600-74347000	Weak transcription	Esophagus	oesophagus
17	chr2:74332800-74346800	Weak transcription	NHEK	skin
18	chr2:74333000-74346800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:74333200-74346800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:74333200-74347000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:74333600-74346600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:74335600-74346800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:74336000-74347000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:74336200-74346600	Weak transcription	Primary T cells from cord blood	blood
25	chr2:74336200-74346600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:74343800-74347000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr2:74344200-74347400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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