Variant report

Variant	rs17624000
Chromosome Location	chr12:41412212-41412213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10506180	0.82[ASN][1000 genomes]
rs10879545	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879622	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11179347	0.83[ASN][1000 genomes]
rs11179395	0.81[ASN][1000 genomes]
rs11179609	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11179834	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11613102	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11614303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12371918	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1388670	0.83[ASN][1000 genomes]
rs2067735	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3794250	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3829303	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3855636	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4767996	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7308370	0.87[ASN][1000 genomes]
rs7311590	0.84[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	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv832382	chr12:41359550-41489681	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv428587	chr12:41375635-41546845	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1051524	chr12:41409977-41643387	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17624000	ZCRB1	cis	parietal	SCAN
rs17624000	GTF3C6	cis	Cerebellum	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41405200-41429800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:41405400-41417600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:41405600-41423000	Weak transcription	Ovary	ovary
4	chr12:41407000-41425200	Weak transcription	Brain Angular Gyrus	brain
5	chr12:41408000-41413000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:41408200-41426400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:41408200-41449800	Weak transcription	Brain Anterior Caudate	brain
8	chr12:41408400-41421400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:41408800-41428000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:41409000-41435000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:41409600-41416800	Weak transcription	A549	lung
12	chr12:41410000-41424800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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