Variant report

Variant	rs2238675
Chromosome Location	chr19:19336608-19336609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr19:19335505-19336820	K562	blood:	n/a	n/a
2	CTCF	chr19:19336460-19336610	AG09319	gingival:	n/a	n/a
3	JUND	chr19:19335912-19336701	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:19334544..19336643-chr19:19365954..19367462,2	K562	blood:
2	chr19:19334243..19337369-chr19:19337755..19340851,3	MCF-7	breast:
3	chr19:19327764..19329892-chr19:19334771..19337455,2	MCF-7	breast:
4	chr19:19309008..19311272-chr19:19335230..19337096,2	MCF-7	breast:
5	chr19:19334594..19337055-chr19:19501477..19503749,2	K562	blood:

No data

Variant related genes	Relation type
NCAN	TF binding region
ENSG00000064490	Chromatin interaction
ENSG00000130287	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2228603	0.81[CHB][hapmap]
rs3761077	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2238675	ZNF714	cis	parietal	SCAN
rs2238675	FAM32A	cis	cerebellum	SCAN
rs2238675	ZNF826P	cis	parietal	SCAN
rs2238675	ZNF99	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19325200-19344600	Weak transcription	Brain Angular Gyrus	brain
2	chr19:19326400-19338400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr19:19326400-19344200	Strong transcription	Brain Germinal Matrix	brain
4	chr19:19326600-19342800	Weak transcription	Fetal Brain Male	brain
5	chr19:19326800-19344200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:19328400-19344400	Strong transcription	Fetal Brain Female	brain
7	chr19:19330400-19344600	Weak transcription	Brain Anterior Caudate	brain
8	chr19:19335000-19339400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:19335200-19344000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:19336200-19336800	Enhancers	Spleen	Spleen
11	chr19:19336400-19336800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr19:19336400-19336800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
13	chr19:19336400-19336800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:19336400-19336800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr19:19336400-19338600	Strong transcription	Brain Cingulate Gyrus	brain
16	chr19:19336400-19338800	Weak transcription	Liver	Liver
17	chr19:19336400-19339000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:19336400-19342800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:19336600-19336800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr19:19336600-19336800	Bivalent Enhancer	HepG2	liver
21	chr19:19336600-19336800	Enhancers	K562	blood
22	chr19:19336600-19337600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:19336600-19338200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:19336600-19339000	Weak transcription	Pancreas	Pancrea

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