Variant report

Variant	rs13174348
Chromosome Location	chr5:115138748-115138749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115137373..115139519-chr5:115171027..115172668,2	K562	blood:
2	chr5:115138361..115140649-chr5:115148381..115150664,2	K562	blood:

Variant related genes	Relation type
ENSG00000129596	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10434761	0.91[ASN][1000 genomes]
rs1058600	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12189155	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12520248	0.91[ASN][1000 genomes]
rs12521324	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154757	0.93[ASN][1000 genomes]
rs154759	0.97[ASN][1000 genomes]
rs258738	0.90[ASN][1000 genomes]
rs26531	0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs26533	0.85[ASN][1000 genomes]
rs26534	0.90[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs26535	0.84[ASN][1000 genomes]
rs26536	0.85[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs26537	0.81[CHB][hapmap]
rs34850	0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs34851	0.90[ASN][1000 genomes]
rs34852	0.90[ASN][1000 genomes]
rs34869	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs35053218	0.97[ASN][1000 genomes]
rs35179959	0.88[ASN][1000 genomes]
rs35903246	0.86[ASN][1000 genomes]
rs3797570	0.90[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs40095	0.90[ASN][1000 genomes]
rs4920892	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57633641	0.87[ASN][1000 genomes]
rs6594906	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6872406	0.90[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6880889	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71581214	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7726368	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13174348	ATG12	cis	cerebellum	SCAN
rs13174348	EPB41L4A	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115131400-115149200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:115134200-115149600	Weak transcription	Ovary	ovary
3	chr5:115134400-115146200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:115134400-115147000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:115134600-115140800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:115135400-115138800	Weak transcription	Brain Germinal Matrix	brain
7	chr5:115136600-115140400	Weak transcription	Fetal Lung	lung
8	chr5:115136800-115144200	Weak transcription	Fetal Brain Male	brain
9	chr5:115137000-115142200	Weak transcription	HepG2	liver
10	chr5:115137200-115142000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:115137400-115139800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:115137600-115139400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:115137600-115143800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:115137800-115140200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:115137800-115147200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:115138000-115143800	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:115138000-115147800	Weak transcription	Fetal Stomach	stomach
18	chr5:115138200-115145000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:115138200-115146200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:115138200-115149200	Weak transcription	Aorta	Aorta
21	chr5:115138200-115149800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:115138400-115139400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:115138400-115139600	Weak transcription	Placenta	Placenta
24	chr5:115138400-115140600	Weak transcription	Fetal Brain Female	brain
25	chr5:115138400-115149800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:115138400-115150800	Weak transcription	Brain Substantia Nigra	brain
27	chr5:115138400-115151000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:115138600-115140000	Genic enhancers	Liver	Liver
29	chr5:115138600-115145800	Strong transcription	Adipose Nuclei	Adipose

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