Variant report

Variant	rs3754748
Chromosome Location	chr2:173938224-173938225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:173937409-173945617	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:173937717-173938880	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	TF binding region
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10180382	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930577	0.88[JPT][hapmap]
rs11681384	0.95[ASN][1000 genomes]
rs11692252	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545516	0.91[ASN][1000 genomes]
rs17760899	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs2034647	0.81[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2044515	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2358084	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754745	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs3769207	0.91[ASN][1000 genomes]
rs6718374	0.99[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6727541	0.84[ASN][1000 genomes]
rs6733082	0.88[ASN][1000 genomes]
rs6735275	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs6758859	0.88[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs6759787	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs7558132	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558553	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7573673	0.82[CEU][hapmap]
rs7608532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9636294	0.83[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs989531	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs989532	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990416	0.99[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs990417	0.98[AFR][1000 genomes];0.90[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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3754748	ZAK	Cis_1M	lymphoblastoid	RTeQTL
rs3754748	METTL8	cis	parietal	SCAN
rs3754748	SCRN3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173934000-173940000	Weak transcription	Pancreas	Pancrea
2	chr2:173935600-173939800	Weak transcription	Fetal Lung	lung
3	chr2:173936000-173940000	Weak transcription	Right Atrium	heart
4	chr2:173937200-173938400	Enhancers	Fetal Heart	heart
5	chr2:173937200-173939600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr2:173937600-173938600	Enhancers	Stomach Smooth Muscle	stomach
7	chr2:173937800-173940000	Weak transcription	Aorta	Aorta
8	chr2:173938000-173938600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:173938000-173938600	Weak transcription	Psoas Muscle	Psoas
10	chr2:173938200-173938400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:173938200-173938600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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