Variant report

Variant	rs6724421
Chromosome Location	chr2:30663110-30663111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10180482	0.93[EUR][1000 genomes]
rs10201729	0.93[EUR][1000 genomes]
rs10202174	0.94[EUR][1000 genomes]
rs13014119	0.91[EUR][1000 genomes]
rs13395754	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1357850	0.91[EUR][1000 genomes]
rs1525063	0.88[EUR][1000 genomes]
rs2076932	0.81[EUR][1000 genomes]
rs28666424	0.86[EUR][1000 genomes]
rs36072623	0.84[EUR][1000 genomes]
rs56150357	0.95[EUR][1000 genomes]
rs62139608	0.92[EUR][1000 genomes]
rs894788	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6724421	LYCAT	Cis_1M	lymphoblastoid	RTeQTL
rs6724421	LYCAT	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30658200-30665600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:30658600-30663600	Enhancers	Fetal Heart	heart
3	chr2:30661400-30663600	Enhancers	Primary T cells from cord blood	blood
4	chr2:30661600-30669400	Weak transcription	Primary B cells from cord blood	blood
5	chr2:30661800-30665400	Weak transcription	K562	blood
6	chr2:30662000-30663600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr2:30662000-30663800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr2:30662200-30663200	Enhancers	Fetal Thymus	thymus
9	chr2:30662400-30663400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr2:30662400-30663400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:30662400-30663600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:30662400-30663600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:30662600-30663200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:30662600-30663200	Enhancers	Thymus	Thymus
15	chr2:30663000-30669400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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Input of quick search could be:

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

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