Variant report

Variant	rs17521900
Chromosome Location	chr1:225516861-225516862
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10799300	0.86[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.81[ASN][1000 genomes]
rs12030277	0.86[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap]
rs12032942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036489	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs12036832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040037	0.86[CHB][hapmap]
rs17522489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3913657	0.86[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap]
rs4653632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv945672	chr1:225339532-225561349	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv873226	chr1:225347689-225555602	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv832703	chr1:225375953-225520216	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv1805729	chr1:225404951-225526778	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2757774	chr1:225404951-225526778	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv2759002	chr1:225404951-225526778	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv428312	chr1:225404951-225526778	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17521900	SUSD4	cis	cerebellum	SCAN
rs17521900	DUSP10	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225507200-225522800	Weak transcription	Fetal Kidney	kidney
2	chr1:225515800-225517400	Enhancers	Hela-S3	cervix
3	chr1:225516400-225517000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:225516600-225517000	Enhancers	HUVEC	blood vessel
5	chr1:225516600-225517200	Enhancers	HMEC	breast
6	chr1:225516600-225517200	Enhancers	NHEK	skin
7	chr1:225516800-225517000	Enhancers	NH-A	brain
8	chr1:225516800-225517200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:225516800-225517200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:225516800-225517400	Enhancers	HSMM	muscle

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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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