Variant report

Variant	rs3108595
Chromosome Location	chr19:37061115-37061116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37041320..37043979-chr19:37059170..37061159,2	K562	blood:
2	chr19:36977340..36979938-chr19:37058785..37061352,2	K562	blood:
3	chr19:37018711..37023188-chr19:37060299..37065354,5	K562	blood:

Variant related genes	Relation type
ENSG00000228629	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10411411	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1053064	0.92[EUR][1000 genomes]
rs12162275	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12973307	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912401	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2912402	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2912406	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2912416	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912417	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967424	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967455	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967470	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3096621	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3096626	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108169	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108170	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108175	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108180	0.89[EUR][1000 genomes]
rs3108198	0.88[EUR][1000 genomes]
rs3108199	0.86[EUR][1000 genomes]
rs3108200	0.88[EUR][1000 genomes]
rs3108207	0.92[EUR][1000 genomes]
rs3108213	0.88[EUR][1000 genomes]
rs3108547	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108548	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108551	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108553	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108554	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108558	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108561	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108571	0.88[EUR][1000 genomes]
rs3108578	0.88[EUR][1000 genomes]
rs3108581	0.88[EUR][1000 genomes]
rs3108587	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108599	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108601	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108611	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3111543	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3111545	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111546	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71337534	0.83[EUR][1000 genomes]
rs7254978	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8112546	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3334779	chr19:37050161-37076919	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3108595	ZNF529	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37021400-37061600	ZNF genes & repeats	Liver	Liver
2	chr19:37022800-37061200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:37023000-37061800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:37023200-37061600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:37023400-37062000	ZNF genes & repeats	Fetal Brain Female	brain
6	chr19:37023400-37063000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:37023800-37061600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:37025600-37062800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:37028600-37061800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr19:37034000-37063000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:37048400-37062800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:37049800-37061800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr19:37050400-37062600	Weak transcription	Fetal Heart	heart
14	chr19:37052800-37063000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:37052800-37063200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:37053400-37063000	Weak transcription	Stomach Mucosa	stomach
17	chr19:37054000-37063200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:37054200-37063000	Weak transcription	Osteobl	bone
19	chr19:37054200-37063800	Weak transcription	Gastric	stomach
20	chr19:37054400-37063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:37055200-37061600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
22	chr19:37055400-37061600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:37055600-37061800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:37055600-37062000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:37055600-37062800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:37055600-37063000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:37055800-37061800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:37056000-37063400	ZNF genes & repeats	A549	lung
29	chr19:37056200-37061600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:37056200-37061600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:37056200-37062800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:37056200-37063000	Weak transcription	Brain Substantia Nigra	brain
33	chr19:37056400-37063000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr19:37056600-37061600	Strong transcription	Placenta	Placenta
35	chr19:37057200-37061200	Weak transcription	NHDF-Ad	bronchial
36	chr19:37057200-37062600	Weak transcription	NHEK	skin
37	chr19:37057200-37062800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:37057200-37063000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:37057400-37061400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:37057400-37061600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:37057400-37063200	Weak transcription	HUVEC	blood vessel
42	chr19:37057600-37062800	Weak transcription	Brain Angular Gyrus	brain
43	chr19:37057800-37062400	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr19:37058000-37063000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:37058200-37061600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:37058200-37061600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:37058400-37062800	Weak transcription	HMEC	breast
48	chr19:37058600-37061800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:37058800-37061400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
50	chr19:37058800-37062400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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