Variant report

Variant	rs939592
Chromosome Location	chr1:151686983-151686984
allele	A/T
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	ZNF263	chr1:151686604-151687882	K562	blood:	n/a	chr1:151687484-151687505 chr1:151687507-151687528 chr1:151687552-151687573 chr1:151686655-151686664
2	ZNF263	chr1:151686317-151687870	HEK293-T-REx	kidney:	n/a	chr1:151687484-151687505 chr1:151687507-151687528 chr1:151687552-151687573 chr1:151686655-151686664

No.	Distal block	Cell Line	Cell type
1	chr1:151677702..151679234-chr1:151685663..151687582,2	K562	blood:
2	chr1:151684278..151687580-chr1:151688035..151691948,5	MCF-7	breast:
3	chr1:151676777..151682969-chr1:151683840..151687385,6	K562	blood:
4	chr1:151685651..151688876-chr1:151692359..151694505,3	MCF-7	breast:
5	chr1:151686149..151687760-chr1:151781194..151783599,2	K562	blood:
6	chr1:151682885..151684895-chr1:151686526..151689556,3	K562	blood:

Variant related genes	Relation type
CELF3	TF binding region
ENSG00000240510	Chromatin interaction
ENSG00000159409	Chromatin interaction
ENSG00000178796	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10218531	0.85[CEU][hapmap]
rs10888431	0.85[CEU][hapmap]
rs10888432	0.81[CEU][hapmap]
rs10888433	0.81[CEU][hapmap]
rs11204879	0.85[CEU][hapmap]
rs11204880	0.85[CEU][hapmap]
rs11808761	0.85[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1196350	0.85[CEU][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap]
rs1196462	0.84[CEU][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs1196466	0.85[CEU][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs1196468	0.81[EUR][1000 genomes]
rs1196469	0.93[YRI][hapmap]
rs12095851	0.85[CEU][hapmap]
rs12122920	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs12128050	0.81[EUR][1000 genomes]
rs12139264	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12723676	0.83[EUR][1000 genomes]
rs12758387	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs1308150	0.93[YRI][hapmap]
rs2096402	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs4043740	0.81[CEU][hapmap]
rs41263702	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845339	0.80[CEU][hapmap];0.87[JPT][hapmap]
rs4845542	0.86[JPT][hapmap]
rs6587615	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes]
rs6587617	0.89[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap]
rs6683687	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6692364	0.81[CEU][hapmap]
rs6696250	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8480	0.81[CEU][hapmap]
rs878775	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs939592	SCNM1	cis	cerebellum	SCAN
rs939592	SPRR2B	cis	cerebellum	SCAN
rs939592	GATAD2B	cis	cerebellum	SCAN
rs939592	FLG2	cis	cerebellum	SCAN
rs939592	LCE1C	cis	parietal	SCAN
rs939592	TDRKH	cis	cerebellum	SCAN
rs939592	LYSMD1	cis	parietal	SCAN
rs939592	BCL9	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151667000-151687400	Weak transcription	K562	blood
2	chr1:151670000-151689800	Weak transcription	Pancreas	Pancrea
3	chr1:151674200-151687400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:151680200-151687400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:151683400-151687800	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
6	chr1:151683400-151688600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:151683800-151687000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:151684000-151687200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
9	chr1:151684400-151687200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:151684400-151687200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:151684400-151689600	Active TSS	Brain Anterior Caudate	brain
12	chr1:151685400-151689800	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr1:151685400-151690000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:151685600-151687000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:151685600-151690400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr1:151685800-151687000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:151685800-151687200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:151685800-151689400	Weak transcription	A549	lung
19	chr1:151686000-151687000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:151686000-151687000	Genic enhancers	Fetal Intestine Small	intestine
21	chr1:151686000-151687000	Enhancers	NHEK	skin
22	chr1:151686000-151687200	Enhancers	HMEC	breast
23	chr1:151686400-151687000	Bivalent Enhancer	HepG2	liver
24	chr1:151686400-151687200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:151686400-151688000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:151686400-151689400	Active TSS	Brain Hippocampus Middle	brain
27	chr1:151686400-151690000	Active TSS	Brain Cingulate Gyrus	brain
28	chr1:151686600-151687800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:151686800-151687000	Flanking Active TSS	Fetal Brain Male	brain
30	chr1:151686800-151687600	Flanking Active TSS	Fetal Intestine Large	intestine
31	chr1:151686800-151690000	Active TSS	Brain Angular Gyrus	brain

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