Variant report

Variant	rs7299744
Chromosome Location	chr12:41318265-41318266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10219754	0.85[AMR][1000 genomes]
rs10784948	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10784951	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10784952	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10784963	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10784965	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10784981	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10879361	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879368	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879384	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879386	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879388	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879390	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879400	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10879415	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10879418	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10879518	0.81[AMR][1000 genomes]
rs10879519	0.84[AMR][1000 genomes]
rs11178978	0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11179084	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11179136	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11179141	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11179142	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11179157	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11179158	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11179184	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11179188	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11179205	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11179237	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11179277	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11179286	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11179300	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11179346	0.87[AMR][1000 genomes]
rs11179364	0.87[AMR][1000 genomes]
rs11179369	0.87[AMR][1000 genomes]
rs11179482	0.84[AMR][1000 genomes]
rs12297682	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12301044	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12301270	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12315093	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12315256	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12367345	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs12578703	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12579817	0.87[AMR][1000 genomes]
rs12580874	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs17624585	0.82[CHB][hapmap]
rs2044090	0.87[AMR][1000 genomes]
rs28581358	0.90[AMR][1000 genomes]
rs7137717	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7305929	0.87[AMR][1000 genomes]
rs7309797	0.87[AMR][1000 genomes]
rs7954108	0.81[AMR][1000 genomes]
rs7958047	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7958050	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7963005	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7968141	0.84[AMR][1000 genomes]
rs7971217	0.84[AMR][1000 genomes]
rs7974854	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs935105	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7299744	CNTN1	cis	cerebellum	SCAN
rs7299744	KIF21A	cis	cerebellum	SCAN
rs7299744	YAF2	cis	parietal	SCAN

Chromatin state (count:10 , 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	chr12:41317400-41318400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:41317800-41356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:41318200-41322200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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