Variant report

Variant	rs7756513
Chromosome Location	chr6:11572817-11572818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11093248..11095637-chr6:11571047..11574245,3	MCF-7	breast:
2	chr6:11536801..11539038-chr6:11570387..11573105,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205269	Chromatin interaction
ENSG00000224531	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11752274	0.94[ASN][1000 genomes]
rs11962387	0.90[AMR][1000 genomes]
rs11962527	0.81[AMR][1000 genomes]
rs11963496	0.84[AMR][1000 genomes]
rs11965815	0.84[AMR][1000 genomes]
rs1522446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16871392	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16871480	0.94[ASN][1000 genomes]
rs17397079	0.90[AMR][1000 genomes]
rs17397134	0.84[AMR][1000 genomes]
rs17397448	0.84[AMR][1000 genomes]
rs17397532	0.84[AMR][1000 genomes]
rs17476088	0.84[AMR][1000 genomes]
rs17476123	0.84[AMR][1000 genomes]
rs17676117	0.83[TSI][hapmap]
rs55635543	0.81[AMR][1000 genomes]
rs55691332	0.81[AMR][1000 genomes]
rs55902701	0.81[AMR][1000 genomes]
rs56104474	0.84[AMR][1000 genomes]
rs56156527	0.84[AMR][1000 genomes]
rs56382227	0.90[AMR][1000 genomes]
rs58875134	0.81[ASN][1000 genomes]
rs59036599	0.81[ASN][1000 genomes]
rs59218333	0.81[ASN][1000 genomes]
rs594164	1.00[CHB][hapmap]
rs59537407	0.81[ASN][1000 genomes]
rs6900342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6900564	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6900578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6900740	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6922363	0.81[ASN][1000 genomes]
rs72834713	0.82[EUR][1000 genomes]
rs72834795	0.81[AMR][1000 genomes]
rs72834796	0.84[AMR][1000 genomes]
rs72834797	0.90[AMR][1000 genomes]
rs72834801	0.84[AMR][1000 genomes]
rs72834802	0.90[AMR][1000 genomes]
rs72836604	0.84[AMR][1000 genomes]
rs72836607	0.90[AMR][1000 genomes]
rs72836611	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72836621	0.84[AMR][1000 genomes]
rs9461825	0.82[EUR][1000 genomes]
rs9469359	0.81[AMR][1000 genomes]
rs9986655	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600989	chr6:11509323-11581990	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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 miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1015234	chr6:11545582-11583516	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7756513	C6orf52	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11557000-11575600	Weak transcription	Spleen	Spleen
2	chr6:11557200-11575400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:11557400-11573200	Weak transcription	Psoas Muscle	Psoas
4	chr6:11563400-11575600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:11564200-11573400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:11565200-11575400	Weak transcription	Right Ventricle	heart
7	chr6:11565800-11575400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:11567000-11579800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:11567200-11573000	Weak transcription	Brain Germinal Matrix	brain
10	chr6:11567400-11575400	Weak transcription	A549	lung
11	chr6:11567600-11575400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:11567600-11575600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:11567600-11575600	Weak transcription	Left Ventricle	heart
14	chr6:11567600-11575600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:11567600-11575800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:11567600-11577400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:11567600-11581400	Weak transcription	Fetal Brain Female	brain
18	chr6:11567600-11582600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:11567600-11586200	Weak transcription	Fetal Intestine Small	intestine
20	chr6:11567600-11586400	Weak transcription	Fetal Stomach	stomach
21	chr6:11567600-11586600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:11567800-11573200	Weak transcription	Lung	lung
23	chr6:11567800-11575400	Weak transcription	Adipose Nuclei	Adipose
24	chr6:11567800-11575600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:11567800-11575600	Weak transcription	Brain Anterior Caudate	brain
26	chr6:11567800-11575600	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:11567800-11575600	Weak transcription	HepG2	liver
28	chr6:11567800-11580000	Weak transcription	Primary B cells from cord blood	blood
29	chr6:11567800-11584200	Weak transcription	HSMMtube	muscle
30	chr6:11567800-11586400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:11568000-11577400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:11568000-11586200	Weak transcription	Liver	Liver
33	chr6:11568000-11586600	Weak transcription	Brain Angular Gyrus	brain
34	chr6:11568200-11575400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:11568200-11575800	Weak transcription	Primary T cells from cord blood	blood
36	chr6:11568200-11578200	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:11568200-11578600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:11568600-11586800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:11569200-11574000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr6:11569400-11574800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr6:11569800-11573000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:11570000-11575400	Weak transcription	GM12878-XiMat	blood
43	chr6:11571200-11574000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:11571600-11573200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:11571600-11575400	Weak transcription	Gastric	stomach
46	chr6:11571800-11575600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:11571800-11586600	Weak transcription	Ovary	ovary
48	chr6:11572400-11575800	Weak transcription	Dnd41	blood
49	chr6:11572800-11573600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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