Variant report

Variant	rs2279447
Chromosome Location	chr15:93013560-93013561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93013260-93014262	H1-neurons	neurons:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM174B-3	chr15:93013469-93013636	XLOC_011583
2	lnc-FAM174B-3	chr15:93013469-93013636	XLOC_011583
3	lnc-FAM174B-3	chr15:93013463-93013636	ENSG00000259170.1
4	lnc-FAM174B-3	chr15:93013391-93013779	NONHSAT048521
5	lnc-FAM174B-3	chr15:93013391-93013636	NONHSAT048520

No data

Variant related genes	Relation type
C15orf32	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11074074	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12441404	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs12592811	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12595501	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs13380006	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs1455772	0.87[ASN][1000 genomes]
rs1455773	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs1455774	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs1455776	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17600420	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784722	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4777990	0.81[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.82[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	nsv948621	chr15:92688981-93158095	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1049561	chr15:92758434-93097965	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
5	nsv519402	chr15:93013560-93015427	Enhancers Weak transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2279447	POLG	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93001400-93015800	Weak transcription	Fetal Brain Male	brain
2	chr15:93008400-93014400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:93010200-93015000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:93011200-93016600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:93011200-93017200	Weak transcription	Fetal Stomach	stomach
6	chr15:93011600-93018000	Weak transcription	HSMMtube	muscle
7	chr15:93011800-93015000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:93011800-93015600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:93012800-93013600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:93012800-93015800	Weak transcription	Spleen	Spleen
11	chr15:93012800-93020800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:93013000-93016400	Weak transcription	Brain Germinal Matrix	brain
13	chr15:93013200-93017200	Weak transcription	Fetal Brain Female	brain

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