Variant report

Variant	rs12576996
Chromosome Location	chr11:65580638-65580639
allele	G/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65478545..65480945-chr11:65580447..65582951,3	MCF-7	breast:
2	chr11:65577404..65580770-chr11:65592566..65594874,3	K562	blood:
3	chr11:65580481..65582382-chr11:65594017..65596909,2	K562	blood:
4	chr11:65478220..65481152-chr11:65579976..65581531,2	MCF-7	breast:
5	chr11:65578671..65581535-chr11:65584408..65587256,5	K562	blood:
6	chr11:65580305..65583287-chr11:65625936..65628715,2	K562	blood:
7	chr11:65483666..65485894-chr11:65578594..65581279,2	MCF-7	breast:
8	chr11:65577980..65580904-chr11:65655568..65657932,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172757	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000175602	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10750772	0.83[ASN][1000 genomes]
rs10896047	0.84[ASN][1000 genomes]
rs10896051	0.83[ASN][1000 genomes]
rs10896052	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs10896073	0.88[JPT][hapmap]
rs11227309	0.83[ASN][1000 genomes]
rs11227311	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs11227318	0.83[ASN][1000 genomes]
rs12575663	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs3892696	1.00[CHB][hapmap]
rs3903072	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs485036	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4930320	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4930326	0.84[ASN][1000 genomes]
rs501630	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs566266	0.83[ASN][1000 genomes]
rs570387	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs633800	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs659824	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs674126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs7107912	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs7123155	0.83[ASN][1000 genomes]
rs735942	0.89[JPT][hapmap]
rs747526	0.89[JPT][hapmap]
rs754532	0.89[JPT][hapmap]
rs7952056	0.89[JPT][hapmap]
rs875311	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv2762915	chr11:65575850-65580638	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12576996	RNASEH2C	cis	parietal	SCAN
rs12576996	CTSF	cis	parietal	SCAN
rs12576996	LRRN4CL	cis	cerebellum	SCAN
rs12576996	SNX32	cis	cerebellum	SCAN
rs12576996	EIF1AD	cis	parietal	SCAN
rs12576996	TSGA10IP	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65574600-65581400	Weak transcription	Fetal Intestine Small	intestine
2	chr11:65575400-65583800	Weak transcription	Brain Substantia Nigra	brain
3	chr11:65576400-65586000	Weak transcription	Spleen	Spleen
4	chr11:65577400-65581200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:65577800-65583200	Enhancers	Adipose Nuclei	Adipose
6	chr11:65577800-65584400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:65578000-65582200	Weak transcription	Left Ventricle	heart
8	chr11:65578000-65584800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr11:65578200-65581600	Weak transcription	Pancreas	Pancrea
10	chr11:65578200-65582400	Weak transcription	Esophagus	oesophagus
11	chr11:65578200-65584400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:65578200-65585200	Weak transcription	Right Ventricle	heart
13	chr11:65578200-65585400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:65578200-65585400	Weak transcription	Gastric	stomach
15	chr11:65578400-65582000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr11:65578600-65585000	Enhancers	Placenta	Placenta
17	chr11:65578800-65584400	Weak transcription	Lung	lung
18	chr11:65579200-65584400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:65579400-65581800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:65579400-65585000	Weak transcription	Primary T cells from cord blood	blood
21	chr11:65579600-65585200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:65579800-65581800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:65579800-65581800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:65579800-65581800	Weak transcription	Right Atrium	heart
25	chr11:65579800-65583800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr11:65579800-65584000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:65580000-65581600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:65580000-65581800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:65580000-65581800	Weak transcription	HSMMtube	muscle
30	chr11:65580000-65584400	Weak transcription	Liver	Liver
31	chr11:65580000-65584400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:65580000-65584600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr11:65580200-65581600	Weak transcription	NHDF-Ad	bronchial
34	chr11:65580200-65585000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:65580400-65582400	Weak transcription	Aorta	Aorta
36	chr11:65580600-65580800	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr11:65580600-65580800	Weak transcription	Hela-S3	cervix
38	chr11:65580600-65585000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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