Variant report

Variant	rs2114447
Chromosome Location	chr15:50567776-50567777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50567739..50569833-chr15:50605430..50607848,2	MCF-7	breast:
2	chr15:50566910..50568792-chr15:50597514..50599198,2	K562	blood:
3	chr15:50567278..50569331-chr15:50646993..50649924,2	K562	blood:
4	chr15:50563105..50566724-chr15:50567713..50571020,4	K562	blood:
5	chr15:50566343..50568625-chr15:50580791..50582388,2	MCF-7	breast:
6	chr15:50561224..50565664-chr15:50565813..50569433,4	MCF-7	breast:
7	chr15:50566525..50568798-chr15:50645931..50647576,2	MCF-7	breast:
8	chr15:50567008..50568947-chr15:50569123..50571870,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10152534	0.98[ASN][1000 genomes]
rs10220734	0.93[ASN][1000 genomes]
rs10220740	0.91[EUR][1000 genomes]
rs10220755	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11633903	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs11638319	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12594956	0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12901373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12913144	0.96[ASN][1000 genomes]
rs1365503	0.91[EUR][1000 genomes]
rs1365504	0.96[ASN][1000 genomes]
rs1797311	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1972699	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2187576	0.85[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs28886692	0.94[ASN][1000 genomes]
rs35777196	0.94[ASN][1000 genomes]
rs3784296	0.91[EUR][1000 genomes]
rs3784297	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3985829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs489345	0.89[ASN][1000 genomes]
rs535648	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs62022573	0.89[ASN][1000 genomes]
rs6493425	1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6493427	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6493430	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs7168233	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8026785	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8030036	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8031431	0.92[ASN][1000 genomes]
rs8039829	0.94[ASN][1000 genomes]
rs8041259	0.95[ASN][1000 genomes]
rs8042451	0.96[ASN][1000 genomes]
rs8042845	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs8043257	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2114447	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs2114447	GABPB1-AS1	cis	Artery Aorta	GTEx
rs2114447	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs2114447	CTD-3110H11.1	cis	lung	GTEx
rs2114447	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2114447	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs2114447	GABPB1-AS1	cis	lung	GTEx
rs2114447	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs2114447	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2114447	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs2114447	CTD-3110H11.1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50555400-50579400	Weak transcription	K562	blood
2	chr15:50558000-50572400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:50558600-50569800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:50564000-50568800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:50564000-50574400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:50564200-50572400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:50564600-50569600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:50566000-50576200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr15:50566000-50580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:50566400-50568000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr15:50566400-50576400	Weak transcription	HUVEC	blood vessel
12	chr15:50566600-50572000	Weak transcription	NHEK	skin
13	chr15:50566800-50569800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:50567000-50569400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr15:50567200-50569800	Weak transcription	Primary T cells from cord blood	blood
16	chr15:50567200-50576200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:50567200-50579600	Weak transcription	Fetal Brain Female	brain
18	chr15:50567200-50579600	Weak transcription	Left Ventricle	heart
19	chr15:50567200-50579600	Weak transcription	Ovary	ovary
20	chr15:50567200-50580000	Weak transcription	Brain Germinal Matrix	brain
21	chr15:50567400-50570600	Weak transcription	Fetal Thymus	thymus
22	chr15:50567400-50579600	Weak transcription	Thymus	Thymus
23	chr15:50567600-50569000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:50567600-50579600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:50567600-50579600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:50567600-50593000	Weak transcription	NHDF-Ad	bronchial

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