Variant report

Variant	rs3995932
Chromosome Location	chr3:112829792-112829793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10511319	0.84[ASN][1000 genomes]
rs10934222	0.87[CHD][hapmap]
rs11712319	0.87[ASN][1000 genomes]
rs11716722	0.83[ASN][1000 genomes]
rs11720141	0.87[ASN][1000 genomes]
rs11923603	0.81[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12490566	0.85[ASN][1000 genomes]
rs12631199	0.87[CHD][hapmap]
rs2178398	0.88[ASN][1000 genomes]
rs4555493	0.89[ASN][1000 genomes]
rs62262801	0.87[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	nsv877344	chr3:112789865-112854339	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv877345	chr3:112826253-112848851	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3995932	BTLA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112808800-112832400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:112819400-112830400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:112824200-112829800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:112825000-112829800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:112825200-112829800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:112826000-112832200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:112826200-112829800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:112827600-112830400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:112828000-112829800	Weak transcription	HMEC	breast
10	chr3:112828000-112830000	Enhancers	Ovary	ovary
11	chr3:112828000-112830200	Enhancers	Fetal Thymus	thymus
12	chr3:112828000-112830400	Enhancers	Fetal Muscle Leg	muscle
13	chr3:112828200-112830000	Weak transcription	NHEK	skin
14	chr3:112828200-112836200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:112828600-112829800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:112828800-112830000	Enhancers	Fetal Muscle Trunk	muscle
17	chr3:112828800-112830200	Enhancers	Fetal Stomach	stomach
18	chr3:112829200-112830000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:112829200-112830200	Enhancers	Colon Smooth Muscle	Colon
20	chr3:112829200-112831200	Enhancers	Hela-S3	cervix
21	chr3:112829400-112829800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:112829400-112829800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:112829400-112830400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr3:112829400-112830400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:112829400-112830400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:112829600-112830000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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