Variant report

Variant	rs2962370
Chromosome Location	chr5:17215444-17215445
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr5:17215425-17215756	GM12878	blood:	n/a	chr5:17215590-17215601
2	RFX5	chr5:17214940-17217355	Hela-S3	cervix:	n/a	chr5:17215164-17215179 chr5:17215164-17215179 chr5:17215164-17215179 chr5:17215163-17215180
3	REST	chr5:17215249-17221561	H1-neurons	neurons:	n/a	chr5:17217790-17217803
4	SMARCC1	chr5:17215434-17217316	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:17203557..17205619-chr5:17213757..17215779,2	K562	blood:

Variant related genes	Relation type
BASP1	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2929710	0.80[TSI][hapmap]
rs2929726	0.80[TSI][hapmap]
rs2956564	0.80[TSI][hapmap]
rs2956566	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking 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 target site	27 gene(s)	inside rSNPs	diseases
2	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv830218	chr5:17093162-17290045	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv4738	chr5:17178267-17223677	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv521697	chr5:17211649-17225333	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv597312	chr5:17214901-17225333	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bipolar disorder with mood-incongruent psychosis	23092984	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2962370	LOC285696	cis	cerebellum	SCAN
rs2962370	MARCH11	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17200000-17216200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:17212000-17215800	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr5:17212400-17215600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:17212400-17216600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:17213400-17216200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:17213600-17216400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:17213600-17222200	Active TSS	Fetal Brain Female	brain
8	chr5:17213800-17216400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:17213800-17217200	Active TSS	Fetal Brain Male	brain
10	chr5:17214000-17216200	Active TSS	Brain Angular Gyrus	brain
11	chr5:17214000-17219800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:17214200-17216200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:17214200-17216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:17214600-17216400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:17214600-17219400	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr5:17214800-17215800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:17214800-17218800	Active TSS	A549	lung
18	chr5:17215000-17216200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:17215000-17217200	Flanking Active TSS	Hela-S3	cervix
20	chr5:17215000-17219400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr5:17215200-17215600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr5:17215200-17215800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:17215200-17216000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:17215200-17217200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr5:17215400-17215600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr5:17215400-17215600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:17215400-17215600	Active TSS	Primary B cells from cord blood	blood
28	chr5:17215400-17215800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr5:17215400-17215800	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr5:17215400-17215800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
31	chr5:17215400-17216000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:17215400-17216800	Active TSS	Brain Hippocampus Middle	brain
33	chr5:17215400-17219800	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr5:17215400-17221000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links