Variant report

Variant	rs11070414
Chromosome Location	chr15:44220396-44220397
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	TEAD4	chr15:44220266-44220810	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr15:44220213-44220857	H1-hESC	embryonic stem cell:	n/a	n/a
3	GTF2F1	chr15:44220243-44220813	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr15:44220095-44220949	H1-hESC	embryonic stem cell:	n/a	chr15:44220803-44220810 chr15:44220355-44220365
5	ZNF143	chr15:44220165-44220754	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr15:44220253-44220632	H1-hESC	embryonic stem cell:	n/a	n/a
7	HDAC2	chr15:44220340-44220623	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAFK	chr15:44220165-44220623	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTBP2	chr15:44220314-44220861	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr15:44220283-44220840	H1-hESC	embryonic stem cell:	n/a	n/a
11	BRCA1	chr15:44220210-44220598	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr15:44220253-44220751	H1-hESC	embryonic stem cell:	n/a	n/a
13	TAF7	chr15:44220249-44220791	H1-hESC	embryonic stem cell:	n/a	n/a
14	NANOG	chr15:44220231-44220633	H1-hESC	embryonic stem cell:	n/a	n/a
15	CEBPB	chr15:44220234-44220813	H1-hESC	embryonic stem cell:	n/a	chr15:44220714-44220722
16	MAX	chr15:44220201-44220928	H1-hESC	embryonic stem cell:	n/a	n/a
17	BCL11A	chr15:44220253-44220614	H1-hESC	embryonic stem cell:	n/a	n/a
18	SP1	chr15:44220133-44220805	H1-hESC	embryonic stem cell:	n/a	chr15:44220493-44220504 chr15:44220353-44220367
19	EP300	chr15:44220125-44220878	H1-hESC	embryonic stem cell:	n/a	n/a
20	TCF12	chr15:44220221-44220814	H1-hESC	embryonic stem cell:	n/a	chr15:44220803-44220810 chr15:44220355-44220365
21	YY1	chr15:44220230-44220886	H1-hESC	embryonic stem cell:	n/a	n/a
22	ATF2	chr15:44220174-44220797	H1-hESC	embryonic stem cell:	n/a	n/a
23	SP1	chr15:44220170-44220793	H1-hESC	embryonic stem cell:	n/a	chr15:44220493-44220504 chr15:44220353-44220367
24	BCL11A	chr15:44220280-44220581	H1-hESC	embryonic stem cell:	n/a	n/a
25	NANOG	chr15:44220185-44220617	H1-hESC	embryonic stem cell:	n/a	n/a
26	YY1	chr15:44220257-44220728	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:44220313-44220757	H1-hESC	embryonic stem cell:	n/a	n/a
28	REST	chr15:44220209-44220453	H1-hESC	embryonic stem cell:	n/a	n/a
29	HDAC2	chr15:44220204-44220757	H1-hESC	embryonic stem cell:	n/a	n/a
30	TBP	chr15:44220357-44220771	H1-hESC	embryonic stem cell:	n/a	n/a
31	CHD2	chr15:44220220-44220899	H1-hESC	embryonic stem cell:	n/a	chr15:44220356-44220366
32	JUN	chr15:44220094-44220615	H1-hESC	embryonic stem cell:	n/a	n/a
33	EGR1	chr15:44220213-44220654	H1-hESC	embryonic stem cell:	n/a	chr15:44220495-44220508
34	SIN3A	chr15:44220200-44220956	H1-hESC	embryonic stem cell:	n/a	chr15:44220825-44220835 chr15:44220337-44220346

Variant related genes	Relation type
FRMD5	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1077421	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1545182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016837	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2016840	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2306674	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2412822	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2412823	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs28548859	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2918945	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2918946	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3742981	0.84[MEX][hapmap]
rs4544217	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs472797	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530074	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs563940	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs589649	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597705	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs638224	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs678513	0.86[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap]
rs747714	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8023508	0.80[MEX][hapmap]
rs8042714	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs920339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11070414	TGM5	cis	Lymphoblastoid	GTEx
rs11070414	TGM5	cis	lymphoblastoid	seeQTL
rs11070414	ADAL	cis	Thyroid	GTEx
rs11070414	ADAL	cis	Nerve Tibial	GTEx
rs11070414	ADAL	cis	Esophagus Muscularis	GTEx
rs11070414	CKMT1A	cis	Esophagus Mucosa	GTEx
rs11070414	ADAL	cis	Artery Tibial	GTEx
rs11070414	ADAL	cis	Adipose Subcutaneous	GTEx
rs11070414	CATSPER2	cis	multi-tissue	Pritchard
rs11070414	LOC440278	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44208800-44222600	Weak transcription	Fetal Brain Female	brain
2	chr15:44211800-44221800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:44211800-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:44212400-44220600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:44212400-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:44213400-44221600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:44214000-44221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:44214000-44224400	Weak transcription	Right Atrium	heart
9	chr15:44214400-44224000	Weak transcription	HSMMtube	muscle
10	chr15:44215800-44221400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:44216400-44220600	Weak transcription	Brain Anterior Caudate	brain
12	chr15:44216600-44222200	Weak transcription	NH-A	brain
13	chr15:44217600-44220600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr15:44217800-44220800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:44217800-44223200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr15:44217800-44223200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr15:44217800-44223200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:44218000-44220800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr15:44218000-44220800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr15:44218000-44221800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:44218000-44223200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:44218000-44225600	Enhancers	Fetal Heart	heart
23	chr15:44218200-44222200	Weak transcription	NHDF-Ad	bronchial
24	chr15:44218200-44222200	Weak transcription	NHLF	lung
25	chr15:44218400-44222200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:44218600-44220400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:44218600-44228400	Enhancers	Brain Substantia Nigra	brain
28	chr15:44218800-44220800	Weak transcription	Brain Angular Gyrus	brain
29	chr15:44218800-44220800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:44219600-44220400	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:44219600-44220600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:44219600-44220800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:44219600-44221200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:44219600-44225000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:44219600-44225000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:44219800-44220400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr15:44219800-44220800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr15:44219800-44221000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr15:44219800-44222200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:44219800-44223200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:44219800-44225200	Weak transcription	NHEK	skin
42	chr15:44220200-44220600	Active TSS	iPS-20b Cell Line	embryonic stem cell

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