Variant report

Variant	rs2291268
Chromosome Location	chr12:56236043-56236044
allele	A/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	JUN	chr12:56235909-56237196	K562	blood:	n/a	chr12:56236787-56236797 chr12:56236787-56236797 chr12:56236787-56236797 chr12:56236788-56236796

No.	Distal block	Cell Line	Cell type
1	chr12:56209321..56212347-chr12:56235221..56238369,3	K562	blood:
2	chr12:56222506..56227501-chr12:56233677..56237355,4	K562	blood:
3	chr12:56224688..56227501-chr12:56233908..56236745,4	K562	blood:
4	chr12:56228843..56232382-chr12:56234016..56237333,4	K562	blood:
5	chr12:56233687..56236115-chr12:56320248..56323583,3	MCF-7	breast:
6	chr12:56220285..56224153-chr12:56233677..56238372,4	K562	blood:
7	chr12:56235299..56237964-chr12:56318777..56323177,4	MCF-7	breast:
8	chr12:56232360..56237326-chr12:56316163..56320896,5	K562	blood:
9	chr12:56234715..56236964-chr12:56319809..56321457,2	K562	blood:

Variant related genes	Relation type
MMP19	TF binding region
ENSG00000257390	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000123342	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000170473	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10876851	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10876852	0.91[AFR][1000 genomes]
rs12372076	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2887998	0.94[ASW][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs7305787	1.00[ASW][hapmap];0.82[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs772262	0.93[ASW][hapmap];0.82[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs7954619	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7954839	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7965333	0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2291268	PFDN5	cis	cerebellum	SCAN
rs2291268	KRT6A	cis	cerebellum	SCAN
rs2291268	GLS2	cis	cerebellum	SCAN
rs2291268	ZNF740	cis	parietal	SCAN
rs2291268	ARHGEF25	cis	parietal	SCAN
rs2291268	MARCH9	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56225400-56236600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56225400-56237000	Weak transcription	GM12878-XiMat	blood
3	chr12:56225800-56236200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:56225800-56244000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:56226000-56236200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:56226200-56236600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:56226800-56241400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:56227000-56236200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:56227400-56236200	Weak transcription	Esophagus	oesophagus
10	chr12:56227600-56241200	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:56229000-56240800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:56229400-56236400	Weak transcription	Thymus	Thymus
13	chr12:56230000-56236600	Weak transcription	Fetal Intestine Large	intestine
14	chr12:56230400-56241000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:56231200-56236400	Weak transcription	Fetal Intestine Small	intestine
16	chr12:56232200-56236200	Enhancers	Placenta	Placenta
17	chr12:56232400-56236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:56232400-56241000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:56233600-56241000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:56233600-56242400	Weak transcription	Spleen	Spleen
21	chr12:56234200-56236600	Weak transcription	Hela-S3	cervix
22	chr12:56234800-56237000	Active TSS	Colonic Mucosa	Colon
23	chr12:56235000-56236200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:56235000-56237200	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr12:56235200-56236200	Weak transcription	Lung	lung
26	chr12:56235200-56236400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:56235200-56236400	Weak transcription	HUVEC	blood vessel
28	chr12:56235200-56236600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:56235200-56237200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr12:56235400-56236200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:56235400-56236200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:56235400-56236600	Active TSS	Gastric	stomach
33	chr12:56235400-56236800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr12:56235600-56236200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:56235600-56236400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:56235600-56236400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:56235600-56236600	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr12:56235600-56236800	Active TSS	Right Atrium	heart
39	chr12:56235600-56237200	Flanking Active TSS	Osteobl	bone
40	chr12:56235600-56237600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:56235800-56236800	Active TSS	Duodenum Mucosa	Duodenum
42	chr12:56235800-56237000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:56235800-56237000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr12:56235800-56237000	Flanking Active TSS	HSMM	muscle
45	chr12:56235800-56237200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
46	chr12:56236000-56236200	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr12:56236000-56236200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:56236000-56236200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:56236000-56236200	Flanking Active TSS	Colon Smooth Muscle	Colon
50	chr12:56236000-56236200	Active TSS	Fetal Stomach	stomach

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