Variant report

Variant	rs55909253
Chromosome Location	chr3:140005120-140005121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56137512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56248764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62266226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62266258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62266259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62267961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62267962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62267963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62267964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62267965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62267972	0.93[EUR][1000 genomes]
rs62267997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62267999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62268001	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6807041	0.93[EUR][1000 genomes]
rs7640659	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432486	chr3:139924092-140049121	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv829740	chr3:139925767-140106169	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv963581	chr3:139998123-140007344	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139995400-140007400	Weak transcription	HSMMtube	muscle
2	chr3:139999600-140015600	Weak transcription	Pancreas	Pancrea
3	chr3:140003600-140009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:140003800-140007400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:140004000-140007200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:140004200-140005200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:140004400-140005600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:140004400-140009200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:140004400-140015600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:140004600-140008800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:140004800-140008800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:140004800-140009200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:140004800-140015600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:140005000-140005800	Enhancers	Ovary	ovary
15	chr3:140005000-140007800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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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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