Variant report

Variant	rs7546431
Chromosome Location	chr1:113869497-113869498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1342652	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1935746	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1935747	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4545335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839311	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4839315	0.91[ASN][1000 genomes]
rs7518024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1009534	chr1:113856612-113920889	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
5	nsv1013228	chr1:113861524-113919893	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1005599	chr1:113861524-113920889	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1012143	chr1:113861524-113930779	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7546431	KCNA2	cis	parietal	SCAN
rs7546431	KIAA1324	cis	parietal	SCAN
rs7546431	AP4B1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113866400-113870200	Weak transcription	Esophagus	oesophagus
2	chr1:113866800-113870200	Enhancers	NHEK	skin
3	chr1:113866800-113870400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:113868000-113869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:113868000-113875200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:113868400-113870400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:113869200-113870400	Enhancers	HMEC	breast

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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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