Variant report

Variant	rs17221044
Chromosome Location	chr4:104372029-104372030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CISD2-3	chr4:104370248-104375195	NONHSAT097630

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10005997	0.92[ASN][1000 genomes]
rs10026360	0.96[ASN][1000 genomes]
rs11946500	0.99[ASN][1000 genomes]
rs1512275	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17033646	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17220904	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17286262	0.92[ASN][1000 genomes]
rs28615487	0.99[ASN][1000 genomes]
rs35091078	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35478417	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4698894	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4699069	0.92[ASN][1000 genomes]
rs4699070	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4699071	1.00[ASN][1000 genomes]
rs57215821	0.92[ASN][1000 genomes]
rs58909279	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62338932	0.89[ASN][1000 genomes]
rs62338936	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533085	0.92[ASN][1000 genomes]
rs6848028	0.92[ASN][1000 genomes]
rs6857044	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72935453	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7671327	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7675703	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv3348747	chr4:104214627-104609795	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv830023	chr4:104333042-104522801	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1006780	chr4:104355981-104855401	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17221044	NHEDC1	cis	cerebellum	SCAN
rs17221044	TET2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104371800-104372800	Enhancers	Muscle Satellite Cultured Cells	--
2	chr4:104371800-104373200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:104371800-104373400	Enhancers	HMEC	breast
4	chr4:104371800-104373600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:104372000-104373200	Enhancers	NHEK	skin

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