Variant report

Variant	rs2292239
Chromosome Location	chr12:56482180-56482181
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56481876-56482814	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:56482168-56482475	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56480065-56483649	HepG2	liver:	n/a	n/a
4	CTCF	chr12:56482118-56482240	MCF-7	breast:	n/a	n/a
5	ZNF263	chr12:56482038-56482441	HEK293-T-REx	kidney:	n/a	chr12:56482309-56482318
6	CTCF	chr12:56482145-56482207	GM12878	blood:	n/a	n/a
7	CTCF	chr12:56482040-56482190	GM06990	blood:	n/a	n/a
8	CTCF	chr12:56482166-56482200	GM20000	blood:	n/a	n/a
9	POLR2A	chr12:56480940-56482549	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:56480932-56482730	HepG2	liver:	n/a	n/a
11	CTCF	chr12:56482112-56482227	GM10266	blood:	n/a	n/a
12	CTCF	chr12:56482160-56482310	WERI-Rb-1	eye:	n/a	n/a
13	POLR2A	chr12:56482173-56482345	HepG2	liver:	n/a	n/a
14	CTCF	chr12:56482164-56482202	HepG2	liver:	n/a	n/a
15	CTCF	chr12:56482100-56482230	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56471198..56482935-chr12:56506922..56516262,73	MCF-7	breast:
2	chr12:56471261..56483436-chr12:56494778..56506435,58	MCF-7	breast:
3	chr12:56475587..56477681-chr12:56479959..56483381,3	K562	blood:
4	chr12:56479547..56482391-chr12:56486376..56489009,4	MCF-7	breast:
5	chr12:56480457..56482671-chr12:56551431..56553649,2	MCF-7	breast:
6	chr12:56366211..56368901-chr12:56482165..56483976,2	MCF-7	breast:
7	chr12:56472197..56476808-chr12:56477200..56483474,8	K562	blood:
8	chr12:56481353..56485182-chr12:56485259..56488237,4	K562	blood:
9	chr12:56480948..56483944-chr12:56582412..56584224,2	MCF-7	breast:
10	chr12:56477785..56480732-chr12:56480999..56482535,2	K562	blood:

No data

Variant related genes	Relation type
ERBB3	TF binding region
ENSG00000170515	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000257411	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000092841	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10876864	0.88[JPT][hapmap]
rs10876870	0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11171739	0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1131017	0.88[JPT][hapmap]
rs1701704	0.86[CEU][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2271194	0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2456973	0.86[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs2640562	0.88[EUR][1000 genomes]
rs2640564	0.81[EUR][1000 genomes]
rs34415530	0.82[EUR][1000 genomes]
rs3741499	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4759229	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61938962	0.83[EUR][1000 genomes]
rs61938963	0.83[EUR][1000 genomes]
rs705696	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs705704	0.86[CEU][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7297175	0.86[ASN][1000 genomes]
rs7302200	0.82[EUR][1000 genomes]
rs7312770	0.86[ASN][1000 genomes]
rs772921	0.86[CEU][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap]
rs773107	0.82[CEU][hapmap]
rs7971751	0.88[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs877636	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

Variant related diseases (count:4)

Disease	PMID	Source
Type 1 diabetes autoantibodies	21829393	GWAS catalog
Type 1 diabetes	19430480	GWAS catalog
Type 1 diabetes	17554260	GWAS catalog
Type 1 diabetes	18978792	GWAS catalog

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2292239	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL
rs2292239	RAB5B	cis	Muscle Skeletal	GTEx
rs2292239	RPS26	cis	lymphoblastoid	seeQTL
rs2292239	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs2292239	RPS26	trans	brain	seeQTL
rs2292239	MYL6B	cis	cerebellum	SCAN
rs2292239	SMARCC2	cis	parietal	SCAN
rs2292239	RPS26	cis	multi-tissue	Pritchard
rs2292239	SUOX	cis	parietal	SCAN
rs2292239	SUOX	cis	cerebellum	SCAN
rs2292239	KRT82	cis	parietal	SCAN
rs2292239	RPS26	cis	brain	seeQTL
rs2292239	TAC3	cis	parietal	SCAN
rs2292239	AC034102.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56474400-56497200	Weak transcription	Right Atrium	heart
2	chr12:56475000-56485600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:56475800-56482400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:56476200-56497200	Weak transcription	Fetal Kidney	kidney
5	chr12:56476400-56483200	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr12:56476600-56487400	Weak transcription	Lung	lung
7	chr12:56476600-56496400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:56476600-56497600	Weak transcription	Small Intestine	intestine
9	chr12:56476800-56487200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:56477000-56497000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:56477000-56497000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:56477600-56496600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:56477800-56485800	Strong transcription	Fetal Stomach	stomach
14	chr12:56477800-56496200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr12:56478600-56496400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:56478800-56482400	Enhancers	K562	blood
17	chr12:56478800-56483000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:56479200-56486400	Weak transcription	Brain Anterior Caudate	brain
19	chr12:56479200-56486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:56479200-56489800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:56479200-56496000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:56479200-56496400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:56479400-56496800	Strong transcription	Fetal Intestine Small	intestine
24	chr12:56479400-56497200	Strong transcription	Fetal Intestine Large	intestine
25	chr12:56480000-56495800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:56480000-56496400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:56480200-56483200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:56480200-56483200	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr12:56480400-56483000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:56480400-56483200	Strong transcription	HepG2	liver
31	chr12:56480400-56493400	Weak transcription	NHEK	skin
32	chr12:56480800-56484600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:56481200-56482400	Strong transcription	HSMMtube	muscle
34	chr12:56481200-56482800	Enhancers	HUVEC	blood vessel
35	chr12:56481200-56483200	Strong transcription	Brain Hippocampus Middle	brain
36	chr12:56481200-56483800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:56481200-56484400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:56481200-56496200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:56481200-56496800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:56481200-56497000	Weak transcription	Hela-S3	cervix
41	chr12:56481400-56482800	Strong transcription	Gastric	stomach
42	chr12:56481400-56492400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:56481600-56482600	Strong transcription	Esophagus	oesophagus
44	chr12:56481600-56482800	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr12:56481600-56482800	Strong transcription	Colonic Mucosa	Colon
46	chr12:56481600-56483600	Strong transcription	Brain Cingulate Gyrus	brain
47	chr12:56481600-56484000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr12:56481600-56484400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:56481600-56496400	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr12:56481600-56496600	Strong transcription	Placenta	Placenta

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