Variant report

Variant	rs1868945
Chromosome Location	chr19:52098461-52098462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr19:52098436-52098489	GM12878	blood:	n/a	n/a
2	ZNF263	chr19:52096973-52098574	HEK293-T-REx	kidney:	n/a	n/a
3	HCFC1	chr19:52097487-52098490	K562	blood:	n/a	n/a
4	MXI1	chr19:52096692-52098484	SK-N-SH	brain:	n/a	n/a
5	REST	chr19:52096678-52098530	H1-neurons	neurons:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52097772..52099435-chr19:52099519..52102447,4	K562	blood:
2	chr19:51869850..51871538-chr19:52096656..52099033,2	K562	blood:
3	chr19:52097873..52100049-chr19:52100051..52101814,3	K562	blood:
4	chr19:51897297..51899400-chr19:52095029..52099296,3	K562	blood:
5	chr19:52073066..52077206-chr19:52096074..52099799,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269388	TF binding region
ENSG00000167765	TF binding region
ENSG00000267808	TF binding region
ENSG00000105497	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000268889	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000269403	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11084092	0.93[ASN][1000 genomes]
rs1868949	0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3794982	0.85[JPT][hapmap]
rs4801881	0.93[ASN][1000 genomes]
rs4802822	0.93[ASN][1000 genomes]
rs7252645	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7252767	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
8	nsv579966	chr19:52075622-52131119	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
9	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
10	nsv9740	chr19:52096231-52107021	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1868945	ZNF135	cis	cerebellum	SCAN
rs1868945	ZNF580	cis	cerebellum	SCAN
rs1868945	ZNF808	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52096600-52098600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:52096600-52098600	Active TSS	A549	lung
3	chr19:52096600-52098800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:52096800-52098600	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr19:52097000-52098600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr19:52097000-52098600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr19:52097200-52098600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:52097400-52098600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:52097400-52098600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:52097600-52098600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:52097800-52098600	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr19:52098000-52098600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:52098000-52098600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:52098000-52098600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:52098000-52098600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:52098000-52098600	Flanking Active TSS	Liver	Liver
17	chr19:52098000-52098600	Flanking Active TSS	Brain Cingulate Gyrus	brain
18	chr19:52098000-52098600	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr19:52098000-52098600	Flanking Active TSS	NHEK	skin
20	chr19:52098000-52098800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr19:52098000-52098800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:52098000-52098800	Flanking Active TSS	Pancreas	Pancrea
23	chr19:52098000-52098800	Flanking Active TSS	K562	blood
24	chr19:52098200-52098600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:52098200-52098600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr19:52098200-52098600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr19:52098200-52098600	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr19:52098200-52098600	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr19:52098200-52098600	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr19:52098200-52098600	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr19:52098200-52098600	Enhancers	Spleen	Spleen
32	chr19:52098200-52098600	Flanking Active TSS	GM12878-XiMat	blood
33	chr19:52098200-52098800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:52098400-52098600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:52098400-52098600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr19:52098400-52098600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:52098400-52098600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:52098400-52098600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr19:52098400-52098600	Enhancers	Primary T cells fromperipheralblood	blood
40	chr19:52098400-52098600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr19:52098400-52098600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr19:52098400-52098600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr19:52098400-52098600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr19:52098400-52098600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:52098400-52098600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:52098400-52098600	Active TSS	Adipose Nuclei	Adipose
47	chr19:52098400-52098600	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr19:52098400-52098600	Enhancers	Fetal Brain Male	brain
49	chr19:52098400-52098600	Active TSS	Fetal Brain Female	brain
50	chr19:52098400-52098600	Enhancers	Fetal Kidney	kidney

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