Variant report

Variant	rs829690
Chromosome Location	chr2:30662023-30662024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30659808..30662413-chr2:30664986..30667717,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11892635	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11904109	0.82[AMR][1000 genomes]
rs1614348	0.88[EUR][1000 genomes]
rs1615605	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662941	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1662942	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1662944	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1662949	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1662955	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1662958	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1723156	0.88[EUR][1000 genomes]
rs1723167	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1723170	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1723175	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462562	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2692041	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35418935	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4952124	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57320824	0.81[AMR][1000 genomes]
rs72853154	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829562	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829570	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829571	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829573	0.86[EUR][1000 genomes]
rs829576	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829577	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829579	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829584	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs829645	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829647	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829648	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829649	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829650	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829651	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829686	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829687	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829689	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829693	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs829690	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30646400-30662600	Weak transcription	Thymus	Thymus
2	chr2:30658200-30665600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:30658600-30663000	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:30658600-30663600	Enhancers	Fetal Heart	heart
5	chr2:30659800-30663000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:30660600-30662400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:30661400-30663600	Enhancers	Primary T cells from cord blood	blood
8	chr2:30661600-30669400	Weak transcription	Primary B cells from cord blood	blood
9	chr2:30661800-30665400	Weak transcription	K562	blood
10	chr2:30662000-30663600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:30662000-30663800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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