Variant report

Variant	rs55947343
Chromosome Location	chr5:61502596-61502597
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11953146	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1508893	0.82[EUR][1000 genomes]
rs2017818	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2910474	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2910476	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2940579	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2940586	0.83[EUR][1000 genomes]
rs2940591	0.82[EUR][1000 genomes]
rs2961836	0.83[EUR][1000 genomes]
rs2961837	0.83[EUR][1000 genomes]
rs2962027	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2962030	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4235491	0.83[EUR][1000 genomes]
rs4498216	0.83[EUR][1000 genomes]
rs4700472	0.81[EUR][1000 genomes]
rs7712470	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv830318	chr5:61415713-61623320	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv11317	chr5:61501951-61555756	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv821303	chr5:61501951-61555756	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55947343	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61501000-61503200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:61501000-61503600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:61501200-61504200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:61502000-61502600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr5:61502200-61502600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:61502200-61502600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:61502200-61502600	Active TSS	Hela-S3	cervix
8	chr5:61502400-61502600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr5:61502400-61502600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr5:61502400-61503600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:61502400-61503600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:61502400-61504200	Weak transcription	H1 BMP4 Derived Trophoblast 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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