Variant report

Variant	rs8102478
Chromosome Location	chr19:18459947-18459948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18456906..18460381-chr19:18460508..18463177,3	K562	blood:
2	chr19:18459596..18462126-chr19:18521424..18523526,2	K562	blood:
3	chr19:18450818..18454298-chr19:18459013..18461176,3	K562	blood:
4	chr19:18450013..18454993-chr19:18455321..18464358,13	K562	blood:
5	chr19:18457626..18460525-chr19:18518722..18521340,2	MCF-7	breast:
6	chr19:18455682..18458836-chr19:18458957..18460579,3	K562	blood:
7	chr19:18458615..18460578-chr19:18524334..18527055,2	MCF-7	breast:
8	chr19:18458959..18461482-chr19:18499425..18502890,3	K562	blood:
9	chr19:18459053..18460566-chr19:18497005..18498537,2	MCF-7	breast:
10	chr19:18432741..18434392-chr19:18458884..18461310,2	MCF-7	breast:
11	chr19:18454817..18456764-chr19:18457999..18460457,2	K562	blood:
12	chr19:18455756..18458835-chr19:18459734..18462087,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000221167	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000130520	Chromatin interaction
ENSG00000130517	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10401774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403547	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415319	1.00[CEU][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421763	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10423237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424419	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059022	1.00[CHB][hapmap]
rs11881039	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882198	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978423	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28503677	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55887446	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104914	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326450	1.00[ASN][1000 genomes]
rs6413435	1.00[CHB][hapmap]
rs6512259	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66732430	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67348050	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251555	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253758	1.00[ASN][1000 genomes]
rs7254789	1.00[CHB][hapmap]
rs7255983	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73009442	1.00[ASN][1000 genomes]
rs8101249	1.00[CHB][hapmap]
rs8102906	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112644	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8102478	PGPEP1	cis	Nerve Tibial	GTEx
rs8102478	PGPEP1	cis	lung	GTEx
rs8102478	PGPEP1	cis	Artery Tibial	GTEx
rs8102478	PGPEP1	cis	Esophagus Muscularis	GTEx
rs8102478	PGPEP1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18452200-18466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:18452200-18466600	Weak transcription	Ovary	ovary
3	chr19:18452200-18468000	Weak transcription	Aorta	Aorta
4	chr19:18452400-18460200	Weak transcription	Osteobl	bone
5	chr19:18452400-18466600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:18452400-18466600	Weak transcription	Right Ventricle	heart
7	chr19:18452400-18468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:18452400-18484800	Weak transcription	Right Atrium	heart
9	chr19:18452600-18461200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:18452600-18464000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:18452600-18466400	Weak transcription	Brain Angular Gyrus	brain
12	chr19:18452600-18466400	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:18452600-18466400	Weak transcription	Fetal Lung	lung
14	chr19:18452600-18466400	Weak transcription	HSMMtube	muscle
15	chr19:18452600-18466600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:18452600-18466600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:18452600-18466600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:18452600-18466600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:18452600-18466600	Weak transcription	Esophagus	oesophagus
20	chr19:18452600-18466800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:18452600-18467200	Weak transcription	Primary B cells from cord blood	blood
22	chr19:18452600-18467400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr19:18452600-18467800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:18452600-18468000	Weak transcription	HSMM	muscle
25	chr19:18452600-18468200	Weak transcription	NHDF-Ad	bronchial
26	chr19:18452600-18476000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr19:18452600-18484400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr19:18452800-18461000	Weak transcription	Fetal Thymus	thymus
29	chr19:18452800-18466400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr19:18452800-18466600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:18452800-18466600	Weak transcription	Pancreas	Pancrea
32	chr19:18452800-18470400	Weak transcription	Small Intestine	intestine
33	chr19:18452800-18484600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:18453200-18460000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:18453200-18466400	Weak transcription	Brain Anterior Caudate	brain
36	chr19:18453400-18460000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:18453400-18461600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:18453400-18466400	Weak transcription	Brain Substantia Nigra	brain
39	chr19:18453400-18466400	Weak transcription	Hela-S3	cervix
40	chr19:18453400-18468000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:18454400-18460200	Weak transcription	K562	blood
42	chr19:18454400-18465600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:18455200-18460200	Weak transcription	GM12878-XiMat	blood
44	chr19:18455200-18464000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr19:18455200-18464400	Weak transcription	Placenta	Placenta
46	chr19:18455200-18466600	Weak transcription	Lung	lung
47	chr19:18455400-18466400	Weak transcription	Adipose Nuclei	Adipose
48	chr19:18455600-18466400	Weak transcription	Brain Germinal Matrix	brain
49	chr19:18455800-18460000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:18455800-18466400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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