Variant report

Variant	rs1258190
Chromosome Location	chr10:50991900-50991901
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10857538	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1258192	0.92[ASN][1000 genomes]
rs1258196	0.83[EUR][1000 genomes]
rs1258197	0.85[EUR][1000 genomes]
rs1258199	0.85[EUR][1000 genomes]
rs1258200	0.85[EUR][1000 genomes]
rs1258201	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1258202	0.86[EUR][1000 genomes]
rs1258203	0.86[EUR][1000 genomes]
rs1258204	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs1258205	0.87[EUR][1000 genomes]
rs1258206	0.87[EUR][1000 genomes]
rs1258207	0.87[EUR][1000 genomes]
rs1258208	0.87[EUR][1000 genomes]
rs1262346	0.87[ASN][1000 genomes]
rs1270159	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34474302	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1048905	chr10:50928727-51019190	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2758219	chr10:50971974-51925166	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv2759749	chr10:50971974-51925166	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv428232	chr10:50971974-51925166	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1258190	AGAP6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50991200-50992800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:50991600-50992000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:50991600-50992200	Enhancers	H9 Cell Line	embryonic stem cell
4	chr10:50991600-50992800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:50991800-50992200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr10:50991800-50992400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr10:50991800-50992400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr10:50991800-50992400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr10:50991800-50992800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:50991800-50993000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:50991800-50993400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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