Variant report

Variant	rs12273601
Chromosome Location	chr11:9636854-9636855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:9481140..9484022-chr11:9635844..9638076,2	MCF-7	breast:
2	chr11:9625140..9628957-chr11:9633939..9638776,5	K562	blood:
3	chr11:9634944..9638366-chr11:9672187..9674812,3	K562	blood:
4	chr11:9635234..9636871-chr11:9761636..9763417,2	MCF-7	breast:
5	chr11:9605204..9607351-chr11:9635673..9637421,2	K562	blood:
6	chr11:9634831..9638731-chr11:9777356..9781938,7	K562	blood:
7	chr11:9479842..9485152-chr11:9633556..9639403,13	K562	blood:
8	chr11:9597111..9603831-chr11:9632388..9638176,11	K562	blood:
9	chr11:9633888..9637224-chr11:9645529..9649937,4	K562	blood:
10	chr11:9634299..9636932-chr11:9637562..9639803,2	MCF-7	breast:
11	chr11:9586513..9589428-chr11:9634913..9638092,4	K562	blood:
12	chr11:9587790..9592116-chr11:9635065..9637852,3	MCF-7	breast:
13	chr11:9593380..9601954-chr11:9626466..9639393,32	K562	blood:
14	chr11:9634859..9637342-chr11:9650481..9653341,3	K562	blood:
15	chr11:9554823..9558413-chr11:9633918..9637025,5	K562	blood:
16	chr11:9634169..9637157-chr11:9770583..9773571,2	MCF-7	breast:
17	chr11:9604448..9606704-chr11:9634785..9637173,2	K562	blood:
18	chr11:9633888..9638474-chr11:9645827..9648910,5	K562	blood:
19	chr11:9594663..9596724-chr11:9636780..9638593,2	K562	blood:
20	chr11:9635657..9637159-chr11:9686246..9687885,2	MCF-7	breast:
21	chr11:9479781..9484865-chr11:9633607..9638660,10	K562	blood:
22	chr11:9586141..9589428-chr11:9634451..9638092,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000245522	Chromatin interaction
ENSG00000255463	Chromatin interaction
ENSG00000268403	Chromatin interaction
ENSG00000238387	Chromatin interaction
ENSG00000166483	Chromatin interaction
ENSG00000243869	Chromatin interaction
ENSG00000246273	Chromatin interaction
ENSG00000243964	Chromatin interaction
ENSG00000166478	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10770047	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840269	0.98[GIH][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10840270	0.93[GIH][hapmap];0.84[MEX][hapmap]
rs10840271	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840274	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs2060477	0.91[ASN][1000 genomes]
rs2289074	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.96[ASN][1000 genomes]
rs57701122	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7105378	0.82[EUR][1000 genomes]
rs7109545	0.91[ASN][1000 genomes]
rs7109585	0.91[ASN][1000 genomes]
rs7118466	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7118581	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7124238	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv896986	chr11:9636854-9679145	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12273601	ENSG00000133789	cis	multi-tissue	Pritchard
rs12273601	SWAP70	Cis_1M	lymphoblastoid	RTeQTL
rs12273601	SWAP70	cis	multi-tissue	Pritchard
rs12273601	SWAP70	cis	lymphoblastoid	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9634400-9637000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:9634600-9637000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:9634600-9637200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr11:9635000-9637000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr11:9635400-9646400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:9635800-9637000	Flanking Active TSS	Hela-S3	cervix
7	chr11:9636000-9637000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr11:9636000-9637400	Flanking Active TSS	GM12878-XiMat	blood
9	chr11:9636200-9637000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr11:9636200-9637000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:9636200-9637000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:9636200-9637000	Enhancers	Brain Cingulate Gyrus	brain
13	chr11:9636200-9637000	Enhancers	Placenta	Placenta
14	chr11:9636200-9637000	Enhancers	Left Ventricle	heart
15	chr11:9636200-9639400	Enhancers	HSMMtube	muscle
16	chr11:9636200-9640000	Enhancers	HSMM	muscle
17	chr11:9636200-9640200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:9636400-9637000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr11:9636400-9637000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:9636400-9637000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:9636400-9637000	Active TSS	Brain Hippocampus Middle	brain
22	chr11:9636400-9637000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr11:9636400-9637000	Enhancers	Fetal Intestine Large	intestine
24	chr11:9636400-9637000	Enhancers	Fetal Intestine Small	intestine
25	chr11:9636400-9637000	Enhancers	Fetal Muscle Trunk	muscle
26	chr11:9636400-9637000	Enhancers	Fetal Thymus	thymus
27	chr11:9636400-9637000	Flanking Active TSS	K562	blood
28	chr11:9636400-9637200	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr11:9636400-9637400	Enhancers	NHLF	lung
30	chr11:9636400-9637800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:9636400-9637800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:9636400-9647400	Weak transcription	Right Atrium	heart
33	chr11:9636600-9637000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr11:9636600-9637000	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr11:9636600-9637000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
36	chr11:9636600-9637000	Enhancers	Primary B cells from cord blood	blood
37	chr11:9636600-9637000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:9636600-9637000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:9636600-9637000	Enhancers	A549	lung
40	chr11:9636600-9637000	Bivalent Enhancer	HepG2	liver
41	chr11:9636600-9637200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr11:9636600-9637200	Enhancers	Primary T cells from cord blood	blood
43	chr11:9636600-9637600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr11:9636600-9637800	Weak transcription	Fetal Kidney	kidney
45	chr11:9636600-9638600	Enhancers	Primary hematopoietic stem cells	blood
46	chr11:9636600-9639400	Weak transcription	NHEK	skin
47	chr11:9636600-9640200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:9636600-9640200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:9636600-9640200	Enhancers	NHDF-Ad	bronchial
50	chr11:9636600-9642200	Enhancers	Primary B cells from peripheral blood	blood

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