Variant report

Variant	rs11690774
Chromosome Location	chr2:190110841-190110842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10497699	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs10931402	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10931406	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10931410	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11675295	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11676812	0.97[EUR][1000 genomes]
rs11678388	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11681937	0.83[EUR][1000 genomes]
rs11684417	0.82[EUR][1000 genomes]
rs11684869	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11687908	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11695837	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12472232	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1515875	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17198773	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17198780	0.82[CEU][hapmap]
rs17198787	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17198815	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17198829	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17198857	0.90[CEU][hapmap]
rs17270952	0.82[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs17270966	0.82[CEU][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs17270973	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs17270987	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17271008	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17271015	0.83[EUR][1000 genomes]
rs35598715	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55851872	0.95[EUR][1000 genomes]
rs56252219	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56381644	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59031473	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61130121	0.91[EUR][1000 genomes]
rs61528955	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62182060	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62182061	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62182066	0.83[EUR][1000 genomes]
rs62182415	0.89[EUR][1000 genomes]
rs62182421	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62182457	0.95[EUR][1000 genomes]
rs62182458	0.94[EUR][1000 genomes]
rs62182459	0.94[EUR][1000 genomes]
rs62183841	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62183844	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62183845	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62183846	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62183847	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62183848	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72908368	0.91[EUR][1000 genomes]
rs72908382	0.91[EUR][1000 genomes]
rs72910347	0.94[EUR][1000 genomes]
rs72910360	0.95[EUR][1000 genomes]
rs72912280	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72912286	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7564429	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7586853	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1014747	chr2:190097979-190132854	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv875614	chr2:190110841-190254758	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11690774	COL5A2	cis	parietal	SCAN
rs11690774	COL5A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190108800-190113800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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