Variant report

Variant	rs7120548
Chromosome Location	chr11:47662932-47662933
allele	C/T
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:13)
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	MXI1	chr11:47662891-47664597	IMR90	lung:	n/a	n/a
2	MYC	chr11:47662599-47665236	K562	blood:	n/a	chr11:47664084-47664093 chr11:47665218-47665227 chr11:47665219-47665226 chr11:47665213-47665228 chr11:47665216-47665227
3	MXI1	chr11:47662753-47664743	SK-N-SH	brain:	n/a	n/a
4	MAX	chr11:47662595-47662958	K562	blood:	n/a	n/a
5	HCFC1	chr11:47662559-47665501	Hela-S3	cervix:	n/a	n/a
6	MYC	chr11:47662762-47663413	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr11:47662932-47663015	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47660129..47661788-chr11:47662493..47664105,2	MCF-7	breast:
2	chr11:47599184..47601918-chr11:47661794..47664226,4	MCF-7	breast:
3	chr11:47661932..47663606-chr11:47755819..47758646,2	K562	blood:
4	chr11:47660831..47663188-chr11:47962801..47965480,2	K562	blood:
5	chr11:47206285..47208872-chr11:47661768..47663771,2	K562	blood:
6	chr11:47661534..47663358-chr11:47740296..47742508,2	K562	blood:
7	chr11:47662615..47664358-chr11:47788211..47790386,2	K562	blood:
8	chr11:47599811..47601701-chr11:47661212..47663329,2	K562	blood:
9	chr11:47599811..47601393-chr11:47661829..47664063,2	K562	blood:
10	chr11:47586161..47588765-chr11:47660200..47662976,2	MCF-7	breast:
11	chr11:47662583..47667763-chr11:47735291..47739208,6	MCF-7	breast:
12	chr11:47662615..47665881-chr11:47786940..47791485,8	K562	blood:
13	chr11:47662579..47666117-chr11:47735408..47738256,8	MCF-7	breast:

No data

Variant related genes	Relation type
MTCH2	TF binding region
ENSG00000109920	Chromatin interaction
ENSG00000110536	Chromatin interaction
ENSG00000123444	Chromatin interaction
ENSG00000231880	Chromatin interaction
ENSG00000109919	Chromatin interaction
ENSG00000149187	Chromatin interaction
ENSG00000213619	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000165923	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1017730	1.00[ASW][hapmap];0.81[CHB][hapmap];0.82[MKK][hapmap]
rs10458914	0.85[ASN][1000 genomes]
rs1056387	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs10742814	0.91[GIH][hapmap];0.95[JPT][hapmap]
rs10742817	0.89[GIH][hapmap];0.84[JPT][hapmap]
rs10742820	0.87[GIH][hapmap];0.88[JPT][hapmap]
rs10769282	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838725	0.82[AMR][1000 genomes]
rs10838726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838731	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838732	0.95[JPT][hapmap]
rs10838736	0.87[ASN][1000 genomes]
rs10838739	0.83[ASN][1000 genomes]
rs10838740	0.89[GIH][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs10838746	0.89[GIH][hapmap];0.88[JPT][hapmap]
rs10838758	0.89[JPT][hapmap]
rs10838759	0.89[JPT][hapmap]
rs10838760	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs10838771	0.89[JPT][hapmap]
rs10838773	0.89[JPT][hapmap]
rs10838774	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs10838777	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs11039244	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11039266	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap]
rs11039280	1.00[JPT][hapmap]
rs11039290	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039297	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039329	0.89[GIH][hapmap];0.89[JPT][hapmap]
rs11039332	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039345	0.89[GIH][hapmap];0.89[JPT][hapmap]
rs11039373	0.89[JPT][hapmap]
rs11039377	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs11039398	0.84[ASN][1000 genomes]
rs11039402	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs11039409	0.82[ASN][1000 genomes]
rs11039419	0.85[JPT][hapmap]
rs12223593	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12226431	0.89[JPT][hapmap]
rs12286721	0.89[GIH][hapmap];0.89[JPT][hapmap]
rs12361415	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap]
rs12365079	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12577383	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12577643	0.88[CEU][hapmap]
rs12785949	0.88[JPT][hapmap]
rs12807014	0.83[AMR][1000 genomes]
rs1563820	0.89[JPT][hapmap]
rs1563821	0.84[JPT][hapmap]
rs2203712	0.95[JPT][hapmap]
rs2242081	0.91[GIH][hapmap];0.95[JPT][hapmap]
rs2280231	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs2290851	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs3740699	0.91[GIH][hapmap];0.84[JPT][hapmap]
rs3758655	0.89[JPT][hapmap]
rs3816605	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs3886262	0.89[JPT][hapmap]
rs4539273	0.89[GIH][hapmap];0.89[JPT][hapmap]
rs4752796	0.84[GIH][hapmap];0.84[JPT][hapmap]
rs4752860	0.89[GIH][hapmap];0.89[JPT][hapmap]
rs4752865	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs6485758	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6485763	0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6485773	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs6485775	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs6485786	0.89[JPT][hapmap]
rs7107792	0.83[ASN][1000 genomes]
rs7107922	0.83[ASN][1000 genomes]
rs7108479	0.89[JPT][hapmap]
rs7110300	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs7114011	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs7114813	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs7118178	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[CHB][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7129797	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7131262	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs71475921	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs754434	0.85[GIH][hapmap];0.89[JPT][hapmap]
rs7927445	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7929014	0.89[GIH][hapmap];0.89[JPT][hapmap]
rs7932703	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs7933019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7936948	0.89[GIH][hapmap];0.89[JPT][hapmap]
rs7939420	0.89[GIH][hapmap];0.89[JPT][hapmap]
rs7945312	0.87[ASN][1000 genomes]
rs7950696	0.95[JPT][hapmap]

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	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv3424537	chr11:47660545-47663980	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7120548	SPI1	cis	multi-tissue	Pritchard
rs7120548	C1QTNF4	cis	lymphoblastoid	seeQTL
rs7120548	FNBP4	cis	lesional skin	skin_eQTL
rs7120548	MTCH2	cis	cerebellum	SCAN
rs7120548	MADD	cis	parietal	SCAN
rs7120548	C1QTNF4	cis	multi-tissue	Pritchard
rs7120548	MYBPC3	cis	multi-tissue	Pritchard
rs7120548	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47637600-47663200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47648200-47663200	Weak transcription	Gastric	stomach
3	chr11:47657000-47663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:47657000-47663200	Weak transcription	Esophagus	oesophagus
5	chr11:47657200-47663400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:47658800-47663200	Weak transcription	Lung	lung
7	chr11:47661000-47663000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:47661200-47663000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:47661200-47663200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:47661400-47663000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr11:47661400-47663200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr11:47661400-47663200	Weak transcription	Placenta	Placenta
13	chr11:47661800-47663000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr11:47661800-47663200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:47662000-47663000	Enhancers	Ovary	ovary
16	chr11:47662000-47663000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr11:47662000-47663200	Enhancers	Small Intestine	intestine
18	chr11:47662000-47663600	Flanking Active TSS	Liver	Liver
19	chr11:47662200-47663000	Enhancers	Brain Angular Gyrus	brain
20	chr11:47662200-47663000	Enhancers	Brain Substantia Nigra	brain
21	chr11:47662200-47663000	Enhancers	Fetal Brain Male	brain
22	chr11:47662200-47663000	Flanking Active TSS	GM12878-XiMat	blood
23	chr11:47662200-47663200	Enhancers	Primary B cells from peripheral blood	blood
24	chr11:47662200-47663200	Enhancers	Primary T cells fromperipheralblood	blood
25	chr11:47662200-47663200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr11:47662200-47663200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:47662200-47663200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr11:47662200-47663200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:47662200-47663200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:47662200-47663200	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr11:47662200-47663400	Flanking Active TSS	Hela-S3	cervix
32	chr11:47662400-47663000	Enhancers	Primary B cells from cord blood	blood
33	chr11:47662400-47663000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr11:47662400-47663000	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr11:47662400-47663000	Enhancers	Fetal Lung	lung
36	chr11:47662400-47663000	Enhancers	Left Ventricle	heart
37	chr11:47662400-47663000	Enhancers	Right Ventricle	heart
38	chr11:47662400-47663000	Active TSS	K562	blood
39	chr11:47662400-47663200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:47662400-47663200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr11:47662400-47663200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr11:47662400-47663200	Flanking Active TSS	HMEC	breast
43	chr11:47662400-47663200	Flanking Active TSS	NHEK	skin
44	chr11:47662400-47663400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:47662400-47663400	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr11:47662400-47663400	Enhancers	Spleen	Spleen
47	chr11:47662400-47663400	Flanking Active TSS	Dnd41	blood
48	chr11:47662400-47664800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:47662400-47664800	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr11:47662600-47663000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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