Variant report

Variant	rs4645927
Chromosome Location	chr11:65482827-65482828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65481809-65482979	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:65481882-65482855	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:65482533-65482849	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr11:65481841-65482849	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr11:65479114-65482970	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:65481810-65482828	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:65481786-65482960	GM12891	blood:	n/a	n/a
8	POLR2A	chr11:65481648-65483024	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:65482465-65482992	K562	blood:	n/a	n/a
10	POLR2A	chr11:65481077-65483114	K562	blood:	n/a	n/a
11	POLR2A	chr11:65481505-65488416	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr11:65481799-65483047	K562	blood:	n/a	n/a
13	POLR2A	chr11:65481633-65482990	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr11:65481903-65482947	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr11:65481647-65482917	U87	brain:	n/a	n/a
16	POLR2A	chr11:65482660-65482940	GM12891	blood:	n/a	n/a
17	POLR2A	chr11:65481527-65483038	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr11:65481900-65482866	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr11:65481765-65482943	HL-60	blood:	n/a	n/a
20	POLR2A	chr11:65481753-65482943	GM12892	blood:	n/a	n/a
21	POLR2A	chr11:65482713-65482914	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr11:65481411-65483476	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65482499..65489390-chr11:65622947..65628870,15	MCF-7	breast:
2	chr11:65482061..65486231-chr11:65638918..65641829,3	K562	blood:
3	chr11:65481897..65483713-chr11:65546531..65549436,2	K562	blood:
4	chr11:65472429..65485450-chr11:65615794..65629774,38	K562	blood:
5	chr11:65477911..65483635-chr11:65545629..65549670,11	K562	blood:
6	chr11:65477884..65488010-chr11:65623516..65630419,28	MCF-7	breast:
7	chr11:65479523..65484500-chr11:65551483..65556601,5	MCF-7	breast:
8	chr11:65480803..65482959-chr11:65822015..65824523,2	MCF-7	breast:

No data

Variant related genes	Relation type
KAT5	TF binding region
ENSG00000172818	Chromatin interaction
ENSG00000172638	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175827	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000254470	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1073602	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1074155	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1074156	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10791822	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896025	0.92[ASN][1000 genomes]
rs10896026	0.92[ASN][1000 genomes]
rs10896028	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896032	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896033	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896034	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10896035	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896037	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10896038	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227251	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227254	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227279	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227281	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227299	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs11532071	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11537193	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11568300	0.93[ASN][1000 genomes]
rs11600918	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11601509	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11604568	0.83[ASN][1000 genomes]
rs11606947	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12225620	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12289836	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12576766	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12802391	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1466462	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2236682	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306362	0.81[ASN][1000 genomes]
rs28464085	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4014192	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4014195	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4645933	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930312	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4930313	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56686587	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60626743	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61893835	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61895665	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6591185	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6591187	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6591188	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7110576	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7115734	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7120713	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7123489	0.86[ASN][1000 genomes]
rs746429	0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs7924510	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7930301	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7947604	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7952133	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs948494	0.92[CEU][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap]
rs9666878	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4645927	DRAP1	cis	parietal	SCAN
rs4645927	RNASEH2C	cis	parietal	SCAN
rs4645927	PCNXL3	cis	cerebellum	SCAN
rs4645927	SIPA1	cis	cerebellum	SCAN
rs4645927	CTSF	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65480000-65487400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65480600-65483000	Genic enhancers	Placenta	Placenta
3	chr11:65480600-65485200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:65480600-65485800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:65480600-65486400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:65480600-65486600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:65480600-65486800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:65480600-65486800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:65480800-65485000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:65480800-65485000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:65480800-65485400	Strong transcription	Psoas Muscle	Psoas
12	chr11:65480800-65485600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:65480800-65485600	Strong transcription	Liver	Liver
14	chr11:65480800-65485600	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr11:65480800-65485600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr11:65480800-65485800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:65480800-65485800	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:65480800-65486000	Strong transcription	Thymus	Thymus
19	chr11:65480800-65486200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:65480800-65486200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:65480800-65486200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr11:65480800-65486200	Strong transcription	Lung	lung
23	chr11:65480800-65486200	Strong transcription	NHEK	skin
24	chr11:65480800-65486200	Strong transcription	NHLF	lung
25	chr11:65480800-65486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:65480800-65486400	Strong transcription	Ovary	ovary
27	chr11:65480800-65486600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:65480800-65486600	Strong transcription	A549	lung
29	chr11:65480800-65486800	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr11:65480800-65486800	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr11:65480800-65486800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr11:65480800-65486800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:65480800-65486800	Strong transcription	Aorta	Aorta
34	chr11:65480800-65487000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:65481000-65484000	Strong transcription	Fetal Kidney	kidney
36	chr11:65481000-65484800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:65481000-65485000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr11:65481000-65485200	Strong transcription	HepG2	liver
39	chr11:65481000-65485400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:65481000-65485400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr11:65481000-65485600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:65481000-65485600	Strong transcription	Colon Smooth Muscle	Colon
43	chr11:65481000-65485800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:65481000-65485800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr11:65481000-65485800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:65481000-65485800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:65481000-65485800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:65481000-65485800	Strong transcription	Adipose Nuclei	Adipose
49	chr11:65481000-65485800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:65481000-65485800	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links