Variant report

Variant	rs2145639
Chromosome Location	chr14:97250576-97250577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10131890	0.93[JPT][hapmap]
rs10132573	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10135222	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10135234	0.94[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs10135283	0.94[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10144908	0.82[ASN][1000 genomes]
rs10145396	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11160369	0.82[CHB][hapmap]
rs11628733	0.82[CHB][hapmap]
rs12589919	0.83[CHD][hapmap]
rs12878184	0.81[CHD][hapmap]
rs12882176	0.97[ASN][1000 genomes]
rs12883251	0.82[ASN][1000 genomes]
rs12897588	0.83[CHD][hapmap]
rs17310204	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1957134	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs1957135	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2145636	0.83[CHD][hapmap]
rs2145638	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2224442	0.82[CHB][hapmap]
rs4633647	0.89[ASN][1000 genomes]
rs4900345	0.82[ASN][1000 genomes]
rs4900346	0.83[CHD][hapmap]
rs4900353	0.83[CHD][hapmap]
rs61980999	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7160250	0.82[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs8009190	0.82[ASN][1000 genomes]
rs912340	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041078	chr14:97001679-97279220	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1050075	chr14:97004951-97279220	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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	nsv1044202	chr14:97155291-97683983	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542179	chr14:97155291-97683983	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv510650	chr14:97238489-97325221	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2145639	SCARNA13	cis	cerebellum	SCAN
rs2145639	C14orf132	cis	parietal	SCAN
rs2145639	VRK1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:97248800-97251400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:97249000-97252600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr14:97249400-97250600	Flanking Active TSS	NHEK	skin
4	chr14:97249400-97251000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr14:97249600-97250800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr14:97249800-97251400	Enhancers	Primary B cells from cord blood	blood
7	chr14:97249800-97251400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr14:97249800-97251400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:97250000-97250800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr14:97250000-97251400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr14:97250200-97251000	Enhancers	HMEC	breast
12	chr14:97250200-97254400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr14:97250400-97251400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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