Variant report

Variant	rs12367345
Chromosome Location	chr12:41421642-41421643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10219754	0.87[ASN][1000 genomes]
rs10784963	0.80[ASN][1000 genomes]
rs10784965	0.80[ASN][1000 genomes]
rs10784981	0.83[ASN][1000 genomes]
rs10879400	0.80[ASN][1000 genomes]
rs10879415	0.80[ASN][1000 genomes]
rs10879418	0.80[ASN][1000 genomes]
rs10879518	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10879519	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10879631	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11179157	0.80[ASN][1000 genomes]
rs11179158	0.80[ASN][1000 genomes]
rs11179184	0.80[ASN][1000 genomes]
rs11179188	0.80[ASN][1000 genomes]
rs11179205	0.80[ASN][1000 genomes]
rs11179237	0.80[ASN][1000 genomes]
rs11179277	0.83[ASN][1000 genomes]
rs11179286	0.83[ASN][1000 genomes]
rs11179300	0.83[ASN][1000 genomes]
rs11179346	0.90[ASN][1000 genomes]
rs11179364	0.90[ASN][1000 genomes]
rs11179369	0.90[ASN][1000 genomes]
rs11179419	0.90[ASN][1000 genomes]
rs11179482	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11179582	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11179592	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11179617	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11179638	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11179687	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11179828	0.89[EUR][1000 genomes]
rs12301270	0.80[ASN][1000 genomes]
rs12315093	0.80[ASN][1000 genomes]
rs12315256	0.80[ASN][1000 genomes]
rs12367206	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12578703	0.80[ASN][1000 genomes]
rs12579817	0.90[ASN][1000 genomes]
rs12580345	0.89[EUR][1000 genomes]
rs12580874	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs12581237	0.89[EUR][1000 genomes]
rs17624585	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2044090	0.90[ASN][1000 genomes]
rs28581358	0.87[ASN][1000 genomes]
rs7137717	0.80[ASN][1000 genomes]
rs7305929	0.90[ASN][1000 genomes]
rs7309797	0.90[ASN][1000 genomes]
rs73116993	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73116997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73121249	0.89[EUR][1000 genomes]
rs73126948	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7954108	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7958047	0.83[ASN][1000 genomes]
rs7963005	0.80[ASN][1000 genomes]
rs7968141	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7971217	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7974854	0.80[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
rs12367345	CNTN1	cis	cerebellum	SCAN
rs12367345	YAF2	cis	parietal	SCAN

Chromatin state (count:15 , 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	chr12:41405600-41423000	Weak transcription	Ovary	ovary
3	chr12:41407000-41425200	Weak transcription	Brain Angular Gyrus	brain
4	chr12:41408200-41426400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:41408200-41449800	Weak transcription	Brain Anterior Caudate	brain
6	chr12:41408800-41428000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:41409000-41435000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:41410000-41424800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:41417000-41427400	Weak transcription	Fetal Lung	lung
10	chr12:41417800-41423000	Weak transcription	Aorta	Aorta
11	chr12:41418000-41424600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:41418600-41422800	Weak transcription	Brain Substantia Nigra	brain
13	chr12:41419600-41422200	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:41421000-41423600	Weak transcription	Fetal Kidney	kidney
15	chr12:41421400-41421800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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