Variant report

Variant	rs12729017
Chromosome Location	chr1:62674507-62674508
allele	C/T
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	POLR2A	chr1:62673753-62674524	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD2	chr1:62673823-62674704	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:62673712-62674973	H1-hESC	embryonic stem cell:	n/a	n/a
4	ATF2	chr1:62674484-62675205	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:62671110-62680443	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:62672293-62675216	H1-hESC	embryonic stem cell:	n/a	n/a
7	GTF2F1	chr1:62673947-62674683	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:62672294-62680406	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000237227	TF binding region
ENSG00000200174	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12725684	0.83[EUR][1000 genomes]
rs12727452	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733177	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12738720	0.82[EUR][1000 genomes]
rs12740634	0.83[EUR][1000 genomes]
rs12742559	0.82[EUR][1000 genomes]
rs12743112	0.82[EUR][1000 genomes]
rs12745952	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12747871	0.82[EUR][1000 genomes]
rs12753338	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12755711	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760006	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123071	1.00[CHB][hapmap]
rs2886644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34637535	0.82[EUR][1000 genomes]
rs4381221	0.80[EUR][1000 genomes]
rs4625314	0.84[JPT][hapmap]
rs7518470	0.81[AMR][1000 genomes];0.86[EUR][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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv870842	chr1:62644118-62679202	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12729017	JUN	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62661000-62675600	Weak transcription	Right Atrium	heart
2	chr1:62664800-62677800	Weak transcription	Placenta	Placenta
3	chr1:62666000-62695400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:62667400-62676200	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr1:62668400-62677200	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr1:62669000-62674600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:62669000-62675600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:62670400-62677200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:62670600-62675400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:62670600-62676200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:62671600-62675400	Weak transcription	Fetal Intestine Small	intestine
12	chr1:62671800-62678200	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr1:62672200-62675600	Weak transcription	Fetal Kidney	kidney
14	chr1:62672200-62677400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr1:62672800-62674800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:62672800-62675000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:62673200-62675400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:62673200-62676400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:62673800-62674600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:62673800-62677200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
21	chr1:62673800-62677200	ZNF genes & repeats	Fetal Lung	lung
22	chr1:62674000-62677200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:62674200-62674600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:62674400-62675000	ZNF genes & repeats	ES-WA7 Cell Line	embryonic stem cell
25	chr1:62674400-62675600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:62674400-62675600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:62674400-62675600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:62674400-62675600	Weak transcription	Fetal Stomach	stomach
29	chr1:62674400-62676800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
30	chr1:62674400-62678800	Weak transcription	Colonic Mucosa	Colon

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