Variant report

Variant	rs1204772
Chromosome Location	chr11:65581579-65581580
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65478545..65480945-chr11:65580447..65582951,3	MCF-7	breast:
2	chr11:65477139..65479296-chr11:65581106..65583170,2	K562	blood:
3	chr11:65581063..65583136-chr14:59275828..59277328,2	MCF-7	breast:
4	chr11:65484062..65489605-chr11:65581322..65585682,6	MCF-7	breast:
5	chr11:65552345..65559376-chr11:65580965..65587386,14	MCF-7	breast:
6	chr11:65580481..65582382-chr11:65594017..65596909,2	K562	blood:
7	chr11:65581575..65585638-chr11:65589269..65592512,3	K562	blood:
8	chr11:65581388..65588369-chr11:65620968..65629930,12	MCF-7	breast:
9	chr11:65546140..65552176-chr11:65581336..65587164,12	MCF-7	breast:
10	chr11:65580305..65583287-chr11:65625936..65628715,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172977	Chromatin interaction
ENSG00000172922	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000255120	Chromatin interaction
ENSG00000175827	Chromatin interaction
ENSG00000172818	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000254470	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10791825	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791826	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10791828	0.82[JPT][hapmap]
rs10896049	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896055	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151515	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1204771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12420336	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13817	0.88[GIH][hapmap]
rs1939212	0.85[GIH][hapmap]
rs4930162	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930322	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930325	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550976	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs558114	0.88[GIH][hapmap]
rs56169730	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58836187	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593982	0.83[MEX][hapmap]
rs601887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603509	0.83[MEX][hapmap]
rs60678003	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895685	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs630303	0.88[GIH][hapmap]
rs635375	0.88[GIH][hapmap]
rs646675	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648732	0.88[GIH][hapmap]
rs652021	0.88[GIH][hapmap]
rs656040	0.88[GIH][hapmap]
rs6591191	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659857	0.88[GIH][hapmap]
rs665306	0.88[GIH][hapmap]
rs668356	0.88[GIH][hapmap]
rs7112754	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7113768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114014	0.84[GIH][hapmap]
rs7114237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924752	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
7	esv998472	chr11:65581362-65585126	Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv555215	chr11:65581579-65676516	Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1204772	MACROD1	cis	parietal	SCAN
rs1204772	NEAT1	cis	lymphoblastoid	seeQTL
rs1204772	CARNS1	cis	cerebellum	SCAN
rs1204772	GPHA2	cis	parietal	SCAN
rs1204772	ANKRD13D	cis	parietal	SCAN
rs1204772	SNORD27	cis	cerebellum	SCAN
rs1204772	EHD1	cis	lymphoblastoid	seeQTL
rs1204772	EFEMP2	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65575400-65583800	Weak transcription	Brain Substantia Nigra	brain
2	chr11:65576400-65586000	Weak transcription	Spleen	Spleen
3	chr11:65577800-65583200	Enhancers	Adipose Nuclei	Adipose
4	chr11:65577800-65584400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:65578000-65582200	Weak transcription	Left Ventricle	heart
6	chr11:65578000-65584800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:65578200-65581600	Weak transcription	Pancreas	Pancrea
8	chr11:65578200-65582400	Weak transcription	Esophagus	oesophagus
9	chr11:65578200-65584400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:65578200-65585200	Weak transcription	Right Ventricle	heart
11	chr11:65578200-65585400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:65578200-65585400	Weak transcription	Gastric	stomach
13	chr11:65578400-65582000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr11:65578600-65585000	Enhancers	Placenta	Placenta
15	chr11:65578800-65584400	Weak transcription	Lung	lung
16	chr11:65579200-65584400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:65579400-65581800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:65579400-65585000	Weak transcription	Primary T cells from cord blood	blood
19	chr11:65579600-65585200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:65579800-65581800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:65579800-65581800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr11:65579800-65581800	Weak transcription	Right Atrium	heart
23	chr11:65579800-65583800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr11:65579800-65584000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:65580000-65581600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:65580000-65581800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:65580000-65581800	Weak transcription	HSMMtube	muscle
28	chr11:65580000-65584400	Weak transcription	Liver	Liver
29	chr11:65580000-65584400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:65580000-65584600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:65580200-65581600	Weak transcription	NHDF-Ad	bronchial
32	chr11:65580200-65585000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr11:65580400-65582400	Weak transcription	Aorta	Aorta
34	chr11:65580600-65585000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:65580800-65582600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:65581200-65581800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:65581200-65582600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr11:65581200-65584400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr11:65581200-65585000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:65581400-65581600	Enhancers	Brain Anterior Caudate	brain
41	chr11:65581400-65581800	Enhancers	Osteobl	bone
42	chr11:65581400-65582400	Enhancers	Fetal Intestine Small	intestine
43	chr11:65581400-65582400	Enhancers	Hela-S3	cervix
44	chr11:65581400-65583200	Enhancers	NHEK	skin
45	chr11:65581400-65583400	Enhancers	Fetal Intestine Large	intestine

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