Variant report

Variant	rs3732812
Chromosome Location	chr3:112863027-112863028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR52-1	chr3:112861197-112863182	XLOC_003220

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10511319	0.84[ASN][1000 genomes]
rs10934222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712319	0.91[ASN][1000 genomes]
rs11716722	0.90[ASN][1000 genomes]
rs11720141	0.91[ASN][1000 genomes]
rs11923603	0.93[CHB][hapmap]
rs12490566	0.84[ASN][1000 genomes]
rs12631163	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12631199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12634099	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2178398	0.88[ASN][1000 genomes]
rs2204788	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2204789	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2700229	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4528911	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4555493	0.89[ASN][1000 genomes]
rs62262801	0.91[ASN][1000 genomes]
rs62264166	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6770160	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs871595	0.85[ASN][1000 genomes]
rs9855348	0.85[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3732812	BTLA	cis	parietal	SCAN
rs3732812	SIDT1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112847800-112866800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:112849400-112865200	Weak transcription	Fetal Stomach	stomach
3	chr3:112852800-112866800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:112855000-112866800	Weak transcription	Pancreas	Pancrea
5	chr3:112858600-112867400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:112861600-112863400	Enhancers	Colon Smooth Muscle	Colon
7	chr3:112862000-112864400	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:112862400-112864400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:112862600-112866200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:112862600-112866600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:112862600-112866800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:112862600-112866800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:112862800-112866000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:112862800-112866400	Weak transcription	NHEK	skin
15	chr3:112862800-112866800	Weak transcription	HMEC	breast
16	chr3:112863000-112863200	Enhancers	Esophagus	oesophagus
17	chr3:112863000-112866400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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