Variant report

Variant	rs2279596
Chromosome Location	chr12:49498751-49498752
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	REST	chr12:49498553-49499072	ECC-1	luminal epithelium:	n/a	chr12:49498795-49498803 chr12:49498797-49498806
2	REST	chr12:49498532-49499030	HL-60	blood:	n/a	chr12:49498795-49498803 chr12:49498797-49498806
3	REST	chr12:49498697-49498906	H1-hESC	embryonic stem cell:	n/a	chr12:49498795-49498803 chr12:49498797-49498806
4	REST	chr12:49498659-49498914	Hela-S3	cervix:	n/a	chr12:49498795-49498803 chr12:49498797-49498806
5	REST	chr12:49498649-49498918	K562	blood:	n/a	chr12:49498795-49498803 chr12:49498797-49498806
6	REST	chr12:49498571-49499022	MCF-7	breast:	n/a	chr12:49498795-49498803 chr12:49498797-49498806
7	REST	chr12:49498677-49498859	H1-hESC	embryonic stem cell:	n/a	chr12:49498795-49498803 chr12:49498797-49498806
8	REST	chr12:49498528-49499088	ECC-1	luminal epithelium:	n/a	chr12:49498795-49498803 chr12:49498797-49498806
9	REST	chr12:49498569-49498968	PFSK-1	brain:	n/a	chr12:49498795-49498803 chr12:49498797-49498806

No.	Distal block	Cell Line	Cell type
1	chr12:49497413..49500186-chr12:49523883..49526530,3	MCF-7	breast:
2	chr12:49497954..49506685-chr12:49522695..49526444,13	MCF-7	breast:
3	chr12:49485049..49487890-chr12:49497361..49499266,3	K562	blood:
4	chr12:49497683..49501522-chr12:49502793..49506157,6	MCF-7	breast:
5	chr12:49493994..49495959-chr12:49498273..49500284,2	K562	blood:
6	chr12:49493937..49507579-chr12:49519161..49528577,46	K562	blood:
7	chr12:49496967..49499814-chr12:49657721..49660285,2	MCF-7	breast:
8	chr12:49481797..49485931-chr12:49494320..49499569,5	MCF-7	breast:

Variant related genes	Relation type
LMBR1L	TF binding region
ENSG00000257346	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000139636	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1039225	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs10747561	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747562	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747563	0.94[CHB][hapmap]
rs10783302	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783304	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783306	0.83[ASN][1000 genomes]
rs10783307	0.83[CEU][hapmap];0.83[ASN][1000 genomes]
rs10783308	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]
rs10875924	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10875928	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]
rs10875931	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs10875934	0.94[CHB][hapmap]
rs11168854	0.82[EUR][1000 genomes]
rs11168857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168862	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168874	0.92[ASN][1000 genomes]
rs11168884	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs11168893	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs11168910	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs11837207	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12228775	0.86[ASN][1000 genomes]
rs12229524	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1476137	0.88[CEU][hapmap];0.92[ASN][1000 genomes]
rs1476138	0.85[ASN][1000 genomes]
rs1874908	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs1991427	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs2047101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162644	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2241727	0.92[ASN][1000 genomes]
rs2334930	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs2753	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35884657	0.83[ASN][1000 genomes]
rs3741621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57853986	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7306084	0.94[CHB][hapmap]
rs73110168	0.85[ASN][1000 genomes]
rs731350	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs7954521	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs7954530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs7957983	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957998	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7958241	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958572	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7959497	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap]
rs7969963	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969967	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7976890	0.92[ASN][1000 genomes]
rs7978448	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978659	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9325145	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs9788139	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9788140	0.81[EUR][1000 genomes];0.91[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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2279596	DDN	cis	Muscle Skeletal	GTEx
rs2279596	TFCP2	cis	parietal	SCAN
rs2279596	C19orf55	trans	cerebellum	SCAN
rs2279596	RHEBL1	cis	parietal	SCAN
rs2279596	POU6F1	cis	parietal	SCAN
rs2279596	RP11-386G11.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49482800-49499200	Weak transcription	Hela-S3	cervix
2	chr12:49489400-49499800	Strong transcription	Fetal Intestine Large	intestine
3	chr12:49489400-49501200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:49489400-49501400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:49489600-49499400	Strong transcription	Fetal Intestine Small	intestine
6	chr12:49489600-49499600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:49489600-49500800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:49489600-49500800	Strong transcription	Thymus	Thymus
9	chr12:49489600-49501200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:49489600-49502800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:49489800-49498800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:49489800-49499400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:49489800-49500000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:49489800-49500600	Strong transcription	Liver	Liver
15	chr12:49489800-49501000	Weak transcription	Fetal Heart	heart
16	chr12:49489800-49502000	Strong transcription	Fetal Stomach	stomach
17	chr12:49490000-49503000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:49490200-49499000	Strong transcription	Fetal Brain Female	brain
19	chr12:49490200-49501200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:49490400-49498800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:49490400-49498800	Strong transcription	Brain Hippocampus Middle	brain
22	chr12:49490400-49499000	Strong transcription	Fetal Thymus	thymus
23	chr12:49490400-49499400	Strong transcription	Brain Anterior Caudate	brain
24	chr12:49490400-49499400	Strong transcription	Ovary	ovary
25	chr12:49490400-49500200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr12:49490400-49500800	Strong transcription	Primary T cells from cord blood	blood
27	chr12:49490400-49500800	Strong transcription	Colonic Mucosa	Colon
28	chr12:49490400-49500800	Strong transcription	HSMMtube	muscle
29	chr12:49490400-49501000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:49490400-49501200	Strong transcription	Primary B cells from cord blood	blood
31	chr12:49490400-49501200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:49490400-49501400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:49490400-49501600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:49490400-49501800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:49490600-49498800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:49490600-49499000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:49490600-49500800	Strong transcription	Brain Cingulate Gyrus	brain
38	chr12:49490600-49500800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:49490600-49500800	Strong transcription	HSMM	muscle
40	chr12:49490600-49501000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:49490600-49501000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:49490600-49501000	Strong transcription	Dnd41	blood
43	chr12:49490600-49501200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr12:49490600-49501200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:49490800-49499200	Strong transcription	NHEK	skin
46	chr12:49490800-49499400	Weak transcription	HMEC	breast
47	chr12:49490800-49499800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:49491000-49498800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:49491200-49501400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr12:49492000-49501200	Strong transcription	Brain Inferior Temporal Lobe	brain

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