Variant report

Variant	rs3752129
Chromosome Location	chr19:52074761-52074762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1125620	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1379284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1585160	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16982846	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453522	0.95[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1962189	0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs2305371	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864106	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864108	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2864109	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752132	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308054	0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6509552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7245838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249641	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8102214	0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs8108872	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111685	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers 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 target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3752129	ZNF175	cis	lymphoblastoid	seeQTL
rs3752129	ZNF71	cis	cerebellum	SCAN
rs3752129	ZNF175	cis	multi-tissue	Pritchard
rs3752129	SBK2	cis	cerebellum	SCAN
rs3752129	ZNF175	cis	Lymphoblastoid	GTEx
rs3752129	ZNF175	cis	Esophagus Muscularis	GTEx
rs3752129	TNNI3	cis	cerebellum	SCAN
rs3752129	ZNF175	Cis_1M	lymphoblastoid	RTeQTL
rs3752129	ZNF808	cis	parietal	SCAN
rs3752129	ZNF175	cis	Artery Tibial	GTEx
rs3752129	ZNF544	cis	parietal	SCAN
rs3752129	FCAR	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52073800-52075000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr19:52073800-52075000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr19:52073800-52075200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:52073800-52075400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr19:52073800-52075800	Active TSS	A549	lung
6	chr19:52074000-52074800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr19:52074000-52074800	Active TSS	Primary hematopoietic stem cells	blood
8	chr19:52074000-52074800	Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr19:52074000-52074800	Active TSS	Adipose Nuclei	Adipose
10	chr19:52074000-52074800	Active TSS	Liver	Liver
11	chr19:52074000-52074800	Active TSS	Thymus	Thymus
12	chr19:52074000-52074800	Active TSS	Monocytes-CD14+_RO01746	blood
13	chr19:52074000-52075000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:52074000-52075000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:52074000-52075000	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr19:52074000-52075000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:52074000-52075000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:52074000-52075000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:52074000-52075000	Active TSS	Brain Anterior Caudate	brain
20	chr19:52074000-52075000	Active TSS	Brain Cingulate Gyrus	brain
21	chr19:52074000-52075000	Active TSS	Brain Hippocampus Middle	brain
22	chr19:52074000-52075000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr19:52074000-52075000	Active TSS	Fetal Brain Female	brain
24	chr19:52074000-52075000	Active TSS	Hela-S3	cervix
25	chr19:52074000-52075000	Active TSS	HMEC	breast
26	chr19:52074000-52075000	Active TSS	NHLF	lung
27	chr19:52074000-52075200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:52074000-52075200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:52074000-52075200	Active TSS	Muscle Satellite Cultured Cells	--
30	chr19:52074000-52075200	Active TSS	Brain Germinal Matrix	brain
31	chr19:52074000-52075200	Active TSS	NHDF-Ad	bronchial
32	chr19:52074000-52075400	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr19:52074000-52075400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:52074000-52075600	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr19:52074000-52075600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr19:52074000-52075800	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr19:52074000-52075800	Active TSS	K562	blood
38	chr19:52074000-52076000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:52074200-52074800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr19:52074200-52074800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:52074200-52074800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr19:52074200-52074800	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr19:52074200-52074800	Active TSS	Fetal Muscle Leg	muscle
44	chr19:52074200-52074800	Active TSS	Rectal Smooth Muscle	rectum
45	chr19:52074200-52074800	Active TSS	HepG2	liver
46	chr19:52074200-52074800	Active TSS	HUVEC	blood vessel
47	chr19:52074200-52075000	Active TSS	Primary T cells from cord blood	blood
48	chr19:52074200-52075000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:52074200-52075000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:52074200-52075000	Active TSS	Brain Angular Gyrus	brain

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