Variant report

Variant	rs12143625
Chromosome Location	chr1:215391840-215391841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10494994	0.84[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs10864168	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120521	0.81[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs11120527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120529	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12094438	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12402782	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12405930	0.82[EUR][1000 genomes]
rs12406223	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12409910	0.96[EUR][1000 genomes]
rs1339397	0.82[EUR][1000 genomes]
rs1339398	0.82[EUR][1000 genomes]
rs1339413	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1416658	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1416659	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1538542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024619	0.81[EUR][1000 genomes]
rs17024624	0.82[EUR][1000 genomes]
rs17024638	0.82[EUR][1000 genomes]
rs17024649	0.82[EUR][1000 genomes]
rs1981211	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2211126	0.82[EUR][1000 genomes]
rs4356021	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4356022	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4384204	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61819677	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819680	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61819705	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61819706	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61819707	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61819708	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61819709	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61819710	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61819711	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61819714	0.82[EUR][1000 genomes]
rs61819716	0.82[EUR][1000 genomes]
rs61819717	0.82[EUR][1000 genomes]
rs61819747	0.82[EUR][1000 genomes]
rs6686529	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs72737240	0.93[ASN][1000 genomes]
rs7549184	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[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	nsv873169	chr1:215264486-215453286	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
2	nsv873170	chr1:215367248-215440975	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12143625	SYT14	cis	parietal	SCAN
rs12143625	ANGEL2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215380600-215408000	Weak transcription	Osteobl	bone
2	chr1:215388600-215408200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:215389200-215401400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:215389400-215393400	Weak transcription	NHDF-Ad	bronchial
5	chr1:215391200-215392000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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