Variant report

Variant	rs3845624
Chromosome Location	chr1:159218266-159218267
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10489848	0.85[ASN][1000 genomes]
rs10489854	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10489855	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11265146	0.85[ASN][1000 genomes]
rs11265154	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11265155	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11265164	0.91[ASN][1000 genomes]
rs12084987	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12087219	0.87[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12121203	0.99[ASN][1000 genomes]
rs12561917	0.85[ASN][1000 genomes]
rs12564837	0.92[ASN][1000 genomes]
rs12568101	0.85[ASN][1000 genomes]
rs16841967	0.87[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2325914	0.83[ASN][1000 genomes]
rs2325915	0.92[ASN][1000 genomes]
rs2494263	1.00[YRI][hapmap]
rs2875781	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3027055	0.91[ASN][1000 genomes]
rs3027056	0.91[ASN][1000 genomes]
rs3027061	0.91[ASN][1000 genomes]
rs3027063	0.91[ASN][1000 genomes]
rs3027074	0.85[ASN][1000 genomes]
rs3027075	0.85[ASN][1000 genomes]
rs3027077	0.85[ASN][1000 genomes]
rs34497749	0.85[ASN][1000 genomes]
rs34757892	0.85[ASN][1000 genomes]
rs35014997	0.85[ASN][1000 genomes]
rs35262301	0.85[ASN][1000 genomes]
rs35921532	0.91[ASN][1000 genomes]
rs4083420	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4498802	0.85[ASN][1000 genomes]
rs60069993	0.99[ASN][1000 genomes]
rs72633670	0.92[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	nsv872487	chr1:159196765-159342439	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv872488	chr1:159218266-159336948	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Inflammatory biomarkers	22291609	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3845624	TFAP2A	trans	cerebellum	SCAN
rs3845624	CD5L	cis	cerebellum	SCAN
rs3845624	CADM3	cis	cerebellum	SCAN
rs3845624	DENND4B	cis	cerebellum	SCAN
rs3845624	THBS3	cis	parietal	SCAN
rs3845624	PPOX	cis	parietal	SCAN
rs3845624	OR6Y1	cis	parietal	SCAN
rs3845624	C1orf189	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159217000-159218400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:159217000-159218400	Enhancers	NHEK	skin
3	chr1:159217200-159218400	Weak transcription	Esophagus	oesophagus
4	chr1:159218200-159218400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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