Variant report

Variant	rs12519395
Chromosome Location	chr5:119951915-119951916
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr5:119951728-119952068	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr5:119951672-119952032	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr5:119951672-119952058	Hela-S3	cervix:	n/a	chr5:119951865-119951878
4	FOSL2	chr5:119951492-119952573	SK-N-SH	brain:	n/a	chr5:119952435-119952443
5	FOS	chr5:119951642-119952470	MCF10A-Er-Src	breast:	n/a	chr5:119952435-119952443
6	FOS	chr5:119951669-119952068	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr5:119951673-119952096	IMR90	lung:	n/a	chr5:119951865-119951878
8	POU5F1	chr5:119951871-119952259	H1-hESC	embryonic stem cell:	n/a	chr5:119952130-119952144
9	POLR2A	chr5:119951843-119952013	ProgFib	skin:	n/a	n/a
10	POLR2A	chr5:119951622-119952031	SK-N-SH	brain:	n/a	n/a
11	STAT3	chr5:119951704-119952031	MCF10A-Er-Src	breast:	n/a	n/a
12	JUND	chr5:119951662-119952124	SK-N-SH	brain:	n/a	n/a
13	MYC	chr5:119951776-119952043	MCF10A-Er-Src	breast:	n/a	n/a
14	TCF12	chr5:119951497-119952683	SK-N-SH	brain:	n/a	n/a
15	STAT3	chr5:119951903-119952054	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr5:119951583-119952603	MCF10A-Er-Src	breast:	n/a	chr5:119952435-119952443
17	MYC	chr5:119951700-119952131	MCF10A-Er-Src	breast:	n/a	n/a
18	FOSL2	chr5:119951693-119952093	SK-N-SH	brain:	n/a	n/a
19	FOS	chr5:119951595-119952575	MCF10A-Er-Src	breast:	n/a	chr5:119952435-119952443
20	STAT3	chr5:119951698-119952009	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr5:119951611-119952023	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PRR16	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10037806	0.96[ASN][1000 genomes]
rs10053278	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10077211	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11241557	0.82[ASN][1000 genomes]
rs12054672	0.82[ASN][1000 genomes]
rs12654348	0.81[ASN][1000 genomes]
rs1375463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1449165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1524559	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs1524564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1960572	0.81[ASN][1000 genomes]
rs2045187	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2124166	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2124167	0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs2168217	0.96[ASN][1000 genomes]
rs2218717	0.80[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2405955	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2405957	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4438902	0.83[ASN][1000 genomes]
rs4895266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6881097	0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs6881962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6891778	0.88[JPT][hapmap]
rs7724401	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs985263	0.86[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830463	chr5:119806643-119968825	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031453	chr5:119843593-120393038	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv948613	chr5:119861955-119999008	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv599602	chr5:119866504-120023393	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv949499	chr5:119869763-119999008	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv830464	chr5:119950090-120106717	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12519395	DMXL1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119942600-119952800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:119948200-119952000	Enhancers	Osteobl	bone
3	chr5:119948600-119952000	Enhancers	HSMM	muscle
4	chr5:119949200-119953000	Enhancers	NHLF	lung
5	chr5:119949400-119952400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:119949400-119953000	Enhancers	HMEC	breast
7	chr5:119949400-119953000	Enhancers	NHEK	skin
8	chr5:119949600-119952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:119949800-119953000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:119950600-119952000	Weak transcription	Aorta	Aorta
11	chr5:119950600-119953000	Enhancers	HSMMtube	muscle
12	chr5:119950600-119954600	Weak transcription	Fetal Lung	lung
13	chr5:119950600-119967400	Weak transcription	Psoas Muscle	Psoas
14	chr5:119950800-119953000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:119950800-119953000	Enhancers	NH-A	brain
16	chr5:119951000-119954400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:119951400-119952400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:119951400-119952800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:119951600-119952000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr5:119951600-119952200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr5:119951600-119952400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr5:119951600-119952400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr5:119951600-119952400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:119951600-119952400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr5:119951600-119952400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:119951600-119952400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:119951600-119952400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:119951600-119952400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr5:119951600-119952600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr5:119951600-119952600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr5:119951600-119952600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr5:119951600-119952600	Flanking Active TSS	NHDF-Ad	bronchial
33	chr5:119951800-119952000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr5:119951800-119952200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:119951800-119952200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:119951800-119952200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:119951800-119952400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr5:119951800-119952400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:119951800-119952400	Enhancers	Hela-S3	cervix
40	chr5:119951800-119952600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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