Variant report

Variant	rs3752133
Chromosome Location	chr19:52049899-52049900
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52030593..52033124-chr19:52048546..52050181,3	K562	blood:
2	chr19:52008070..52014830-chr19:52047100..52054399,12	K562	blood:
3	chr19:52041105..52042982-chr19:52048290..52051568,3	K562	blood:
4	chr19:52048879..52051552-chr19:52072033..52076241,4	K562	blood:
5	chr19:52048957..52051581-chr19:52070091..52071870,2	K562	blood:
6	chr19:52048446..52051862-chr19:52097608..52099669,3	K562	blood:
7	chr19:52049354..52051242-chr19:52535429..52537065,2	K562	blood:
8	chr19:52008381..52014764-chr19:52049250..52052653,6	K562	blood:
9	chr19:51950650..51953356-chr19:52049895..52051617,2	K562	blood:
10	chr19:51869528..51871905-chr19:52048389..52050215,2	K562	blood:
11	chr19:52035935..52037669-chr19:52048715..52051154,2	K562	blood:
12	chr19:51795590..51798270-chr19:52046982..52049972,2	K562	blood:
13	chr19:52048080..52051637-chr19:52074741..52078887,5	K562	blood:
14	chr19:52049091..52052644-chr19:52057964..52061166,6	K562	blood:
15	chr19:51982494..51986261-chr19:52048308..52051566,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105497	Chromatin interaction
ENSG00000105492	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000167765	Chromatin interaction
ENSG00000105379	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000269580	Chromatin interaction
ENSG00000268839	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10401247	0.83[ASN][1000 genomes]
rs10426927	0.82[ASN][1000 genomes]
rs1457093	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1840826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124908	0.93[EUR][1000 genomes]
rs3794982	0.80[CEU][hapmap]
rs7252645	0.80[CEU][hapmap]
rs8102214	0.82[CHB][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3752133	ZNF175	cis	brain	seeQTL
rs3752133	ZNF175	cis	multi-tissue	Pritchard
rs3752133	ZNF175	cis	lymphoblastoid	seeQTL
rs3752133	SIGLEC12	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52047200-52052400	Enhancers	Primary B cells from peripheral blood	blood
2	chr19:52047400-52050400	Enhancers	Primary hematopoietic stem cells	blood
3	chr19:52048800-52058000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:52049000-52050000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:52049000-52051000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:52049000-52051200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:52049000-52052000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr19:52049200-52050000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr19:52049200-52050000	Flanking Active TSS	K562	blood
10	chr19:52049200-52051000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:52049200-52051000	Enhancers	Placenta	Placenta
12	chr19:52049400-52051400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr19:52049600-52050000	Flanking Active TSS	GM12878-XiMat	blood
14	chr19:52049600-52050600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr19:52049800-52050000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:52049800-52050000	Bivalent Enhancer	Primary T cells from cord blood	blood
17	chr19:52049800-52050000	Flanking Active TSS	HUVEC	blood vessel
18	chr19:52049800-52050000	Flanking Active TSS	Osteobl	bone
19	chr19:52049800-52050800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr19:52049800-52051000	Enhancers	Fetal Thymus	thymus
21	chr19:52049800-52053000	Enhancers	Stomach Mucosa	stomach

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