Variant report

Variant	rs1218551
Chromosome Location	chr1:154801173-154801174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1010225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1218552	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1218553	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1218598	1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs2798604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv464050	chr1:154568683-154801247	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv547958	chr1:154568683-154801247	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1218551	SNAPIN	cis	parietal	SCAN
rs1218551	OTUD7B	cis	parietal	SCAN
rs1218551	RXFP4	cis	cerebellum	SCAN
rs1218551	SPRR1A	cis	parietal	SCAN
rs1218551	RAG1AP1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154786600-154801800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:154787000-154805400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:154792800-154805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:154793600-154803600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:154794600-154802800	Weak transcription	Right Ventricle	heart
6	chr1:154796000-154801800	Weak transcription	Brain Anterior Caudate	brain
7	chr1:154796400-154801200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:154797400-154801600	Weak transcription	Fetal Brain Female	brain
9	chr1:154797400-154801600	Weak transcription	Psoas Muscle	Psoas
10	chr1:154797800-154803200	Weak transcription	Fetal Brain Male	brain
11	chr1:154797800-154803200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:154799200-154801600	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:154799200-154803600	Weak transcription	Fetal Stomach	stomach
14	chr1:154800600-154801800	Enhancers	Fetal Muscle Leg	muscle
15	chr1:154800800-154801200	Enhancers	HSMMtube	muscle
16	chr1:154801000-154801800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:154801000-154802200	Enhancers	GM12878-XiMat	blood

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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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