Variant report

Variant	rs551708
Chromosome Location	chr11:66486143-66486144
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66445330..66447437-chr11:66485877..66488287,2	MCF-7	breast:
2	chr11:66485179..66487927-chr11:66610525..66613195,2	MCF-7	breast:
3	chr11:66483106..66491369-chr11:66506993..66514506,29	MCF-7	breast:
4	chr11:66473019..66474925-chr11:66484776..66487058,2	K562	blood:
5	chr11:66453297..66456868-chr11:66484727..66488184,5	MCF-7	breast:
6	chr11:66459760..66463831-chr11:66485092..66488454,5	MCF-7	breast:
7	chr11:66485734..66487264-chr11:66489137..66490968,2	K562	blood:
8	chr11:66485277..66487714-chr11:67007342..67009981,2	MCF-7	breast:
9	chr11:66464517..66466889-chr11:66484801..66487417,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173653	Chromatin interaction
ENSG00000173120	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000173898	Chromatin interaction
ENSG00000173715	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10750790	0.83[CEU][hapmap]
rs10791889	0.83[CEU][hapmap]
rs12795774	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap]
rs1987169	0.93[ASN][1000 genomes]
rs2077432	0.82[CEU][hapmap]
rs2242663	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs2513658	0.82[TSI][hapmap]
rs481296	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs484262	0.82[ASW][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.83[YRI][hapmap]
rs4930390	0.83[CEU][hapmap]
rs508996	0.95[ASN][1000 genomes]
rs532439	0.86[GIH][hapmap]
rs543191	0.89[TSI][hapmap]
rs569818	0.89[TSI][hapmap]
rs594313	0.89[TSI][hapmap]
rs608248	0.89[TSI][hapmap]
rs610293	0.85[JPT][hapmap]
rs624561	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.84[ASN][1000 genomes]
rs627330	0.89[TSI][hapmap]
rs682842	0.89[TSI][hapmap]
rs7570	0.82[CEU][hapmap]
rs7930203	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv897791	chr11:66442855-66533469	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv897792	chr11:66486143-66529101	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv897793	chr11:66486143-66533469	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs551708	EHBP1L1	cis	cerebellum	SCAN
rs551708	ESRRA	cis	cerebellum	SCAN
rs551708	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs551708	SYT12	cis	parietal	SCAN
rs551708	IGHMBP2	cis	parietal	SCAN
rs551708	ACTN3	cis	Muscle Skeletal	GTEx
rs551708	CCS	cis	lymphoblastoid	seeQTL
rs551708	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs551708	SLC25A45	cis	parietal	SCAN
rs551708	C11orf80	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66456400-66494600	Weak transcription	Right Atrium	heart
2	chr11:66465600-66487000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:66468800-66487800	Strong transcription	Fetal Brain Female	brain
4	chr11:66469600-66486800	Weak transcription	A549	lung
5	chr11:66471600-66489200	Strong transcription	Brain Germinal Matrix	brain
6	chr11:66478400-66486600	Weak transcription	Hela-S3	cervix
7	chr11:66481600-66487000	Weak transcription	HMEC	breast
8	chr11:66481800-66487200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:66481800-66493400	Weak transcription	Fetal Brain Male	brain
10	chr11:66482200-66486600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:66482600-66487000	Weak transcription	Spleen	Spleen
12	chr11:66482600-66494600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:66482800-66486600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:66482800-66488000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:66482800-66492600	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:66483000-66486800	Weak transcription	Brain Angular Gyrus	brain
17	chr11:66483200-66486800	Weak transcription	K562	blood
18	chr11:66483200-66487600	Weak transcription	Brain Anterior Caudate	brain
19	chr11:66483200-66487800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:66483200-66488000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:66483400-66486200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:66483400-66486600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:66483600-66486200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:66484400-66487800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:66484600-66486600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:66484800-66486400	Active TSS	Esophagus	oesophagus
27	chr11:66484800-66486600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:66485000-66486400	Flanking Active TSS	Liver	Liver
29	chr11:66485000-66486400	Flanking Active TSS	Pancreas	Pancrea
30	chr11:66485000-66486400	Flanking Active TSS	NHEK	skin
31	chr11:66485000-66486800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:66485000-66487400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:66485000-66487400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:66485000-66488800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:66485000-66490600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:66485200-66486400	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr11:66485200-66487000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:66485200-66488000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:66485400-66486200	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr11:66485400-66486200	Active TSS	Gastric	stomach
41	chr11:66485400-66486400	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr11:66485400-66486600	Enhancers	Colonic Mucosa	Colon
43	chr11:66485400-66487200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr11:66485400-66488400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:66485400-66488400	Enhancers	Stomach Mucosa	stomach
46	chr11:66485600-66486200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr11:66485600-66486600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:66485600-66486600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr11:66485600-66487000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr11:66485600-66487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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