Variant report

Variant	rs62357569
Chromosome Location	chr5:40820158-40820159
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10064650	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1070444	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11740266	0.83[AMR][1000 genomes]
rs11743132	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743196	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745121	0.83[AMR][1000 genomes]
rs11746535	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748087	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748743	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749180	0.83[AMR][1000 genomes]
rs11749437	0.83[AMR][1000 genomes]
rs11749955	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12186450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188129	0.83[AMR][1000 genomes]
rs12188981	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12189463	0.83[AMR][1000 genomes]
rs35999176	0.83[AMR][1000 genomes]
rs62356519	0.83[AMR][1000 genomes]
rs62357560	0.83[AMR][1000 genomes]
rs62357568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357570	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357574	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62357600	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704034	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
3	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62357569	CARD6	cis	Artery Tibial	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40808400-40826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:40808800-40825600	Weak transcription	HSMM	muscle
3	chr5:40813200-40823600	Weak transcription	K562	blood
4	chr5:40814000-40821600	Weak transcription	Thymus	Thymus
5	chr5:40814200-40826000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:40814200-40826000	Weak transcription	GM12878-XiMat	blood
7	chr5:40814200-40826400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:40814400-40825000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:40814400-40825200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:40814600-40827000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:40816600-40826600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:40816600-40826800	Weak transcription	Brain Angular Gyrus	brain
13	chr5:40817400-40821600	Weak transcription	Fetal Thymus	thymus
14	chr5:40818600-40826600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:40818600-40827000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:40818800-40825200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:40818800-40826200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:40819000-40825200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:40819000-40825600	Weak transcription	NH-A	brain
20	chr5:40819000-40825600	Weak transcription	NHLF	lung
21	chr5:40819400-40826600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:40819600-40821200	Weak transcription	Fetal Brain Female	brain
23	chr5:40819600-40826600	Weak transcription	Primary B cells from cord blood	blood
24	chr5:40820000-40826400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr5:40820000-40826600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:40820000-40826800	Weak transcription	Brain Hippocampus Middle	brain

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