Variant report

Variant	rs10879365
Chromosome Location	chr12:41322756-41322757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10879367	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879371	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11179116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12304408	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304414	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128962	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7957480	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832380	chr12:41132306-41323961	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	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
3	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
rs10879365	CNTN1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41297200-41338600	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:41297400-41328600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:41297400-41338600	Weak transcription	Brain Angular Gyrus	brain
4	chr12:41297400-41346400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:41305800-41336200	Weak transcription	NHEK	skin
6	chr12:41313400-41338400	Weak transcription	A549	lung
7	chr12:41316400-41327400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:41317800-41356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:41318400-41341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:41318600-41334400	Weak transcription	Fetal Lung	lung
11	chr12:41320000-41324400	Weak transcription	Fetal Brain Male	brain
12	chr12:41321800-41344600	Weak transcription	Ovary	ovary
13	chr12:41322200-41324600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:41322200-41324800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr12:41322400-41322800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr12:41322400-41323000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr12:41322400-41324400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr12:41322400-41336000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:41322600-41323000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr12:41322600-41323000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr12:41322600-41323000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr12:41322600-41323000	Weak transcription	Brain Anterior Caudate	brain
23	chr12:41322600-41324600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:41322600-41337800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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