Variant report

Variant	rs7957480
Chromosome Location	chr12:41331797-41331798
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10879365	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879368	0.84[AFR][1000 genomes]
rs10879371	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11179084	0.83[AFR][1000 genomes]
rs11179116	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304408	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12304414	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17128962	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935105	0.84[AFR][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	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	nsv826346	chr12:41313148-41374833	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7957480	CNTN1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41297200-41338600	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:41297400-41338600	Weak transcription	Brain Angular Gyrus	brain
3	chr12:41297400-41346400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:41305800-41336200	Weak transcription	NHEK	skin
5	chr12:41313400-41338400	Weak transcription	A549	lung
6	chr12:41317800-41356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:41318400-41341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:41318600-41334400	Weak transcription	Fetal Lung	lung
9	chr12:41321800-41344600	Weak transcription	Ovary	ovary
10	chr12:41322400-41336000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:41322600-41337800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:41328200-41338600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:41329200-41337600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:41330600-41332800	Weak transcription	Fetal Brain Female	brain
15	chr12:41330800-41333200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:41331000-41332000	Strong transcription	Brain Anterior Caudate	brain
17	chr12:41331400-41333200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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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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