Variant report

Variant	rs7969091
Chromosome Location	chr12:49464449-49464450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr12:49463183-49464481	GM12878	blood:	n/a	chr12:49463943-49463955
2	JUN	chr12:49462658-49464482	K562	blood:	n/a	chr12:49463943-49463955
3	POLR2A	chr12:49463075-49464517	PFSK-1	brain:	n/a	n/a
4	MTA3	chr12:49462900-49464527	GM12878	blood:	n/a	n/a
5	NR2F2	chr12:49463204-49464540	K562	blood:	n/a	n/a
6	TAF1	chr12:49463848-49464452	PFSK-1	brain:	n/a	n/a
7	RUNX3	chr12:49463270-49464464	GM12878	blood:	n/a	chr12:49464044-49464053 chr12:49464044-49464053 chr12:49464045-49464060

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49446392..49469923-chr12:49518127..49527853,66	K562	blood:
2	chr12:49462406..49465445-chr12:49657502..49661212,4	K562	blood:
3	chr12:49464358..49466907-chr12:49658719..49661076,2	MCF-7	breast:
4	chr12:49462171..49464996-chr12:49523872..49525977,3	MCF-7	breast:
5	chr12:49452319..49453848-chr12:49464029..49465894,2	MCF-7	breast:
6	chr12:49462517..49467862-chr12:49502773..49505660,4	MCF-7	breast:
7	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
8	chr12:49410463..49414527-chr12:49462417..49465664,5	K562	blood:
9	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
10	chr12:49462240..49465825-chr12:49663317..49667869,4	K562	blood:
11	chr12:49460491..49475559-chr12:49480736..49489831,23	K562	blood:

No data

Variant related genes	Relation type
RHEBL1	TF binding region
ENSG00000123416	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000257346	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10459221	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459232	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054442	0.85[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10783299	0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10783300	0.85[ASN][1000 genomes]
rs10783301	0.94[ASN][1000 genomes]
rs10875908	0.85[ASN][1000 genomes]
rs10875910	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10875911	0.85[ASN][1000 genomes]
rs10875912	0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10875913	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10875914	0.85[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.88[ASN][1000 genomes]
rs10875915	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10875917	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875918	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168822	0.82[ASN][1000 genomes]
rs11168827	0.81[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs11168838	0.99[ASN][1000 genomes]
rs11168839	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11168850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1138908	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11614738	0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12298884	0.91[ASN][1000 genomes]
rs12580349	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs12821008	0.95[ASN][1000 genomes]
rs2117029	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2241726	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs2293445	0.84[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2293446	0.85[ASN][1000 genomes]
rs2304275	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34436857	0.94[ASN][1000 genomes]
rs3741619	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs3741622	0.91[JPT][hapmap]
rs3782357	0.81[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6580698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7296288	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs7300136	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs876333	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7969091	NCKAP5L	cis	parietal	SCAN
rs7969091	RHEBL1	cis	parietal	SCAN
rs7969091	DDN	cis	Muscle Skeletal	GTEx
rs7969091	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs7969091	RHEBL1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49463400-49464600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:49464000-49464600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:49464200-49466000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:49464400-49464600	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:49464400-49464600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr12:49464400-49464800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:49464400-49464800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:49464400-49464800	Enhancers	Dnd41	blood
9	chr12:49464400-49465000	Enhancers	Primary hematopoietic stem cells	blood
10	chr12:49464400-49465200	Weak transcription	K562	blood
11	chr12:49464400-49465400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:49464400-49466000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:49464400-49466200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:49464400-49466400	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links