Variant report

Variant	rs55887446
Chromosome Location	chr19:18446868-18446869
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	chr19:18446849-18446952	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:18446841-18446960	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18445090..18448208-chr19:18450045..18453418,4	K562	blood:
2	chr19:18441208..18448128-chr19:18448861..18453326,10	K562	blood:

Variant related genes	Relation type
PGPEP1	TF binding region
ENSG00000130517	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10401774	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415319	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415765	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421763	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881039	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882198	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978423	1.00[ASN][1000 genomes]
rs28503677	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326450	1.00[ASN][1000 genomes]
rs6512259	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66732430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67348050	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251555	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253758	1.00[ASN][1000 genomes]
rs7255983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73009442	1.00[ASN][1000 genomes]
rs8102478	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102906	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112644	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
5	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases
6	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55887446	PGPEP1	cis	Adipose Subcutaneous	GTEx
rs55887446	PGPEP1	cis	Esophagus Muscularis	GTEx
rs55887446	PGPEP1	cis	Nerve Tibial	GTEx
rs55887446	PGPEP1	cis	Artery Tibial	GTEx
rs55887446	PGPEP1	cis	lung	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18434800-18450600	Weak transcription	Spleen	Spleen
2	chr19:18440000-18450600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:18440400-18450600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:18440400-18450600	Weak transcription	Stomach Mucosa	stomach
5	chr19:18440400-18450600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:18440400-18450800	Weak transcription	Right Ventricle	heart
7	chr19:18440600-18448000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr19:18440600-18449000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr19:18440600-18450800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:18441000-18448000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr19:18444000-18450800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:18444200-18451000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:18445000-18450600	Weak transcription	K562	blood
14	chr19:18445000-18450800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:18445000-18451000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:18446200-18448400	Enhancers	HepG2	liver
17	chr19:18446400-18447000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:18446400-18447200	Enhancers	Fetal Intestine Small	intestine
19	chr19:18446400-18447400	Enhancers	Fetal Intestine Large	intestine
20	chr19:18446600-18450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:18446600-18450600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:18446600-18450600	Weak transcription	Placenta	Placenta
23	chr19:18446600-18451000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:18446800-18447200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr19:18446800-18447400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:18446800-18450600	Weak transcription	Lung	lung
27	chr19:18446800-18450800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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