Variant report

Variant	rs1372542
Chromosome Location	chr12:41324876-41324877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10879356	0.80[ASN][1000 genomes]
rs10879360	0.81[EUR][1000 genomes]
rs10879395	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879396	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879417	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879421	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879450	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11178982	0.89[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs11179040	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11179042	0.80[ASN][1000 genomes]
rs11179168	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12296676	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1372538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372544	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1442188	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1442189	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1442192	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17621741	0.89[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs17622354	0.86[AFR][1000 genomes]
rs2289522	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278918	0.82[ASN][1000 genomes]
rs278919	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278920	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794247	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3794248	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816251	0.81[EUR][1000 genomes]
rs391052	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767994	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4767995	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56294359	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7311085	0.84[ASN][1000 genomes]
rs7314287	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7955172	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][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
rs1372542	GXYLT1	cis	cerebellum	SCAN

Chromatin state (count:15 , 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	chr12:41321800-41344600	Weak transcription	Ovary	ovary
12	chr12:41322400-41336000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:41322600-41337800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:41323000-41327000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:41323200-41331000	Weak transcription	Brain Anterior Caudate	brain

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