Variant report

Variant	rs556595
Chromosome Location	chr11:66058082-66058083
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr11:66054844-66061017	SK-N-SH	brain:	n/a	chr11:66060557-66060572
2	REST	chr11:66056386-66058149	PANC-1	pancreas:	n/a	chr11:66057185-66057198 chr11:66057182-66057202 chr11:66057182-66057191 chr11:66057178-66057188
3	REST	chr11:66055981-66058437	HL-60	blood:	n/a	chr11:66057185-66057198 chr11:66057182-66057202 chr11:66057182-66057191 chr11:66057178-66057188
4	REST	chr11:66055927-66058165	K562	blood:	n/a	chr11:66057182-66057191 chr11:66057178-66057188 chr11:66057185-66057198 chr11:66057182-66057202
5	POLR2A	chr11:66054040-66060816	H1-neurons	neurons:	n/a	n/a
6	REST	chr11:66055803-66058221	A549	lung:	n/a	chr11:66057185-66057198 chr11:66057182-66057202 chr11:66057182-66057191 chr11:66057178-66057188
7	RCOR1	chr11:66055391-66058178	IMR90	lung:	n/a	n/a
8	POLR2A	chr11:66055102-66058883	HepG2	liver:	n/a	n/a
9	HCFC1	chr11:66054469-66058486	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:66055262-66058392	HepG2	liver:	n/a	n/a
11	REST	chr11:66055942-66058110	PFSK-1	brain:	n/a	chr11:66057185-66057198 chr11:66057182-66057202 chr11:66057182-66057191 chr11:66057178-66057188
12	REST	chr11:66056298-66058381	PFSK-1	brain:	n/a	chr11:66057185-66057198 chr11:66057182-66057202 chr11:66057182-66057191 chr11:66057178-66057188

No.	Distal block	Cell Line	Cell type
1	chr11:66053947..66059144-chr11:66077550..66083439,18	K562	blood:
2	chr11:66054859..66059696-chr11:66135983..66141726,7	K562	blood:
3	chr11:66006716..66009009-chr11:66056097..66058334,2	MCF-7	breast:
4	chr11:66056831..66061115-chr11:66109718..66114909,6	MCF-7	breast:
5	chr11:66055291..66058281-chr11:66079576..66082924,5	MCF-7	breast:
6	chr11:66055397..66059696-chr11:66135983..66139913,5	K562	blood:
7	chr11:66054909..66058395-chr11:66084021..66087571,3	K562	blood:
8	chr11:66034858..66038328-chr11:66053749..66060447,9	MCF-7	breast:
9	chr11:66056386..66058686-chr11:66082623..66084625,3	MCF-7	breast:
10	chr11:66056885..66058669-chr11:66106452..66107991,2	K562	blood:

Variant related genes	Relation type
YIF1A	TF binding region
TMEM151A	TF binding region
ENSG00000254762	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000174807	Chromatin interaction
ENSG00000254458	Chromatin interaction
ENSG00000174744	Chromatin interaction
ENSG00000174903	Chromatin interaction
ENSG00000174669	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10791865	0.97[GIH][hapmap]
rs10896104	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1115508	0.82[EUR][1000 genomes]
rs1151537	0.82[EUR][1000 genomes]
rs1151539	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1151540	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1203798	0.84[EUR][1000 genomes]
rs1717669	0.85[EUR][1000 genomes]
rs1892939	0.86[EUR][1000 genomes]
rs2508657	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3016319	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs474005	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs521109	0.88[EUR][1000 genomes]
rs524859	0.85[GIH][hapmap]
rs528842	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs555360	0.83[EUR][1000 genomes]
rs708471	0.82[EUR][1000 genomes]
rs708472	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs801731	0.81[EUR][1000 genomes]
rs801734	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs801736	0.83[EUR][1000 genomes]
rs801737	0.82[EUR][1000 genomes]
rs801739	0.82[EUR][1000 genomes]
rs801741	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs9326370	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897773	chr11:66041807-66063654	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv555223	chr11:66041807-66064126	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv897774	chr11:66042962-66063654	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv897775	chr11:66042962-66064850	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv897776	chr11:66042962-66066349	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv897777	chr11:66044882-66063654	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv897778	chr11:66044882-66066349	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv897779	chr11:66047523-66063654	Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs556595	PACS1	cis	parietal	SCAN
rs556595	MRGPRF	cis	parietal	SCAN
rs556595	C11orf2	cis	parietal	SCAN
rs556595	RAB1B	cis	parietal	SCAN
rs556595	DKFZp761E198	cis	lymphoblastoid	seeQTL
rs556595	SNX32	cis	parietal	SCAN
rs556595	RAB1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66056000-66061800	Active TSS	Brain Angular Gyrus	brain
2	chr11:66056800-66058200	Flanking Active TSS	Dnd41	blood
3	chr11:66057000-66058800	Bivalent Enhancer	Fetal Brain Male	brain
4	chr11:66057200-66058400	Flanking Active TSS	Brain Anterior Caudate	brain
5	chr11:66057200-66058400	Flanking Active TSS	Hela-S3	cervix
6	chr11:66057200-66058800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
7	chr11:66057400-66058200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:66057400-66058200	Flanking Bivalent TSS/Enh	HepG2	liver
9	chr11:66057400-66058400	Flanking Active TSS	Brain Cingulate Gyrus	brain
10	chr11:66057400-66058400	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr11:66057400-66058400	Flanking Active TSS	Brain Substantia Nigra	brain
12	chr11:66057400-66059000	Weak transcription	Aorta	Aorta
13	chr11:66057600-66058200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr11:66057600-66058200	Enhancers	Pancreas	Pancrea
15	chr11:66057600-66058400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:66057600-66058400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr11:66057600-66058400	Enhancers	Stomach Mucosa	stomach
18	chr11:66057600-66058600	Enhancers	Fetal Intestine Large	intestine
19	chr11:66057600-66058600	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr11:66057600-66058800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr11:66057600-66058800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr11:66057600-66058800	Enhancers	Gastric	stomach
23	chr11:66057600-66059000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:66057600-66059000	Enhancers	Right Ventricle	heart
25	chr11:66057800-66058200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr11:66057800-66058200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:66057800-66058200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:66057800-66058400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:66057800-66058800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr11:66057800-66059000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
31	chr11:66057800-66059000	Bivalent Enhancer	Fetal Intestine Small	intestine
32	chr11:66057800-66059000	Weak transcription	Lung	lung
33	chr11:66057800-66059200	Weak transcription	Ovary	ovary
34	chr11:66058000-66058200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:66058000-66058200	Bivalent Enhancer	Fetal Heart	heart
36	chr11:66058000-66058200	Enhancers	A549	lung
37	chr11:66058000-66058200	Enhancers	K562	blood
38	chr11:66058000-66058400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:66058000-66058400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:66058000-66058800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:66058000-66059000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr11:66058000-66059000	Weak transcription	Esophagus	oesophagus
43	chr11:66058000-66059000	Weak transcription	Left Ventricle	heart
44	chr11:66058000-66059000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr11:66058000-66059000	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links