Variant report

Variant	rs2742115
Chromosome Location	chr12:10322182-10322183
allele	A/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	MXI1	chr12:10321761-10322223	Hela-S3	cervix:	n/a	n/a
2	EP300	chr12:10321656-10322191	Hela-S3	cervix:	n/a	n/a
3	EP300	chr12:10321592-10322241	T-47D	breast:	n/a	n/a
4	SP1	chr12:10321590-10322193	A549	lung:	n/a	n/a
5	EP300	chr12:10321547-10322278	A549	lung:	n/a	n/a
6	POLR2A	chr12:10321554-10325230	Hela-S3	cervix:	n/a	n/a
7	FOXA1	chr12:10322098-10322283	T-47D	breast:	n/a	n/a
8	USF2	chr12:10321968-10322317	Hela-S3	cervix:	n/a	n/a
9	GATA3	chr12:10322045-10322285	T-47D	breast:	n/a	n/a
10	RFX5	chr12:10321762-10323173	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
TMEM52B	TF binding region
OLR1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10845054	0.82[AMR][1000 genomes]
rs10845055	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11053653	0.99[ASN][1000 genomes]
rs12581931	0.82[AMR][1000 genomes]
rs2010655	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2537777	0.92[MEX][hapmap]
rs2537778	0.91[MEX][hapmap]
rs2634159	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2634160	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2634162	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2742107	0.97[ASN][1000 genomes]
rs2742108	0.97[ASN][1000 genomes]
rs2742110	0.82[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs2742112	0.81[ASN][1000 genomes]
rs2742113	0.82[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs2742114	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3741860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4103869	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6488265	0.83[MEX][hapmap]
rs71457827	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7305138	0.95[CHB][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap]
rs7315498	0.87[MEX][hapmap]
rs9300224	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2742115	ACRBP	cis	parietal	SCAN
rs2742115	PTPN6	cis	cerebellum	SCAN
rs2742115	OLR1	cis	multi-tissue	Pritchard
rs2742115	CRTC3	trans	cerebellum	SCAN
rs2742115	CD27	cis	parietal	SCAN
rs2742115	NANOGNB	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10318800-10323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:10319000-10322800	Enhancers	Hela-S3	cervix
3	chr12:10319200-10326200	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr12:10320400-10322600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:10320600-10322200	Weak transcription	HMEC	breast
6	chr12:10320800-10322800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:10320800-10323200	Weak transcription	Primary B cells from cord blood	blood
8	chr12:10321600-10322200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:10321600-10322800	Flanking Active TSS	A549	lung
10	chr12:10321800-10322200	Active TSS	Brain Hippocampus Middle	brain
11	chr12:10321800-10322600	Weak transcription	Placenta	Placenta
12	chr12:10321800-10322800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr12:10321800-10323000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:10321800-10324800	Weak transcription	NHLF	lung
15	chr12:10321800-10331200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:10322000-10322400	Weak transcription	NHEK	skin
17	chr12:10322000-10327600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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