Variant report

Variant	rs769040
Chromosome Location	chr13:92010657-92010658
allele	C/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:62)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:62 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr13:92007619..92012079-chr13:92329462..92332464,5	K562	blood:
2	chr13:92010635..92015807-chr13:92018550..92023163,4	MCF-7	breast:
3	chr13:81121825..81124571-chr13:92009979..92011924,2	K562	blood:
4	chr13:92010540..92013547-chr13:92187635..92190322,4	K562	blood:
5	chr13:91919276..91922212-chr13:92009101..92012516,4	K562	blood:
6	chr13:92009670..92013881-chr13:92375334..92379387,4	K562	blood:
7	chr13:91926747..91928257-chr13:92010434..92012597,2	K562	blood:
8	chr13:91795824..91797926-chr13:92010509..92012771,2	K562	blood:
9	chr13:92010191..92014540-chr13:92229897..92231842,4	K562	blood:
10	chr13:91828167..91832824-chr13:92009386..92012550,6	K562	blood:
11	chr13:92008919..92012229-chr13:92298232..92301726,3	K562	blood:
12	chr13:92009207..92010760-chr13:108629119..108630812,2	K562	blood:
13	chr13:91893680..91897355-chr13:92007107..92011169,4	K562	blood:
14	chr13:92009651..92011564-chr13:92135642..92137218,2	K562	blood:
15	chr11:27882899..27885879-chr13:92008840..92011260,2	K562	blood:
16	chr13:92009199..92012102-chr13:108655339..108657320,2	K562	blood:
17	chr13:91751114..91752648-chr13:92010500..92012399,2	K562	blood:
18	chr13:92006350..92012037-chr13:92182700..92187101,6	K562	blood:
19	chr13:91785773..91787520-chr13:92009738..92011792,2	K562	blood:
20	chr13:92010436..92012496-chr13:92953050..92954701,2	K562	blood:
21	chr13:91830095..91832824-chr13:92009386..92012550,3	K562	blood:
22	chr13:92008998..92011983-chr13:92367729..92370311,3	K562	blood:
23	chr13:92007575..92011337-chr13:92428230..92431057,3	K562	blood:
24	chr13:92009144..92010827-chr13:92120030..92122675,2	K562	blood:
25	chr13:91893680..91896156-chr13:92009275..92010984,2	K562	blood:
26	chr13:92009349..92012461-chr13:92224404..92227397,3	K562	blood:
27	chr13:92009180..92011434-chr13:92452798..92454691,2	K562	blood:
28	chr13:92008212..92012126-chr13:92101857..92105185,4	K562	blood:
29	chr1:8928064..8929777-chr13:92008313..92011039,2	K562	blood:
30	chr13:92010067..92012640-chr9:133779649..133782513,2	K562	blood:
31	chr13:92009525..92012032-chr13:92219135..92221631,2	K562	blood:
32	chr13:91737954..91740404-chr13:92008929..92011702,2	K562	blood:
33	chr13:92009508..92013495-chr13:92125822..92129742,3	K562	blood:
34	chr13:91999461..92007353-chr13:92008154..92015149,15	MCF-7	breast:
35	chr13:92008416..92011064-chr13:92130907..92133015,2	K562	blood:
36	chr13:91916595..91918707-chr13:92008662..92010951,3	K562	blood:
37	chr13:91851245..91855773-chr13:92007361..92011020,5	K562	blood:
38	chr13:91852326..91855280-chr13:92009520..92011626,2	K562	blood:
39	chr13:92010600..92013246-chr13:92212301..92213807,2	K562	blood:
40	chr13:91796426..91798959-chr13:92009042..92012009,2	K562	blood:
41	chr13:92009446..92011873-chr13:92285779..92287489,2	K562	blood:
42	chr13:92007364..92011025-chr13:92217645..92220635,3	K562	blood:
43	chr13:92010398..92013351-chr13:108550982..108553660,2	K562	blood:
44	chr13:92009151..92011579-chr9:134051171..134054051,2	K562	blood:
45	chr13:92009300..92011060-chr13:92144900..92147559,2	K562	blood:
46	chr13:92009784..92014607-chr13:92111183..92117003,5	K562	blood:
47	chr13:91779070..91780625-chr13:92008658..92010674,2	K562	blood:
48	chr13:91822565..91824120-chr13:92010009..92011711,2	K562	blood:
49	chr13:92008301..92012941-chr13:92190227..92194060,8	K562	blood:
50	chr13:92009908..92012117-chr2:43452729..43454781,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204257	Chromatin interaction
ENSG00000152518	Chromatin interaction
ENSG00000179399	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000204256	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1428	0.81[YRI][hapmap]
rs4142965	0.88[YRI][hapmap]
rs9560777	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.87[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	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv832679	chr13:91859467-92030220	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1943 gene(s)	inside rSNPs	diseases
7	esv1802171	chr13:91999737-92015977	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1940 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs769040	GPC6	cis	cerebellum	SCAN
rs769040	GPC5	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92001600-92010800	Weak transcription	Pancreas	Pancrea
2	chr13:92001600-92012200	Weak transcription	Esophagus	oesophagus
3	chr13:92001800-92015600	Weak transcription	Ovary	ovary
4	chr13:92001800-92027200	Weak transcription	Aorta	Aorta
5	chr13:92002000-92011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr13:92002000-92011200	Weak transcription	Colonic Mucosa	Colon
7	chr13:92002000-92012200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:92002200-92010800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr13:92002400-92010800	Weak transcription	Brain Angular Gyrus	brain
10	chr13:92002400-92012000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr13:92003400-92014000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr13:92003600-92010800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr13:92003600-92010800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:92003600-92010800	Strong transcription	HSMM	muscle
15	chr13:92003600-92011800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr13:92003600-92012000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr13:92003600-92012600	Weak transcription	Brain Substantia Nigra	brain
18	chr13:92003600-92012800	Weak transcription	Small Intestine	intestine
19	chr13:92003600-92016600	Weak transcription	Gastric	stomach
20	chr13:92003600-92021200	Weak transcription	Right Ventricle	heart
21	chr13:92003600-92033200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr13:92003800-92011000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:92003800-92011800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr13:92003800-92012200	Strong transcription	Fetal Thymus	thymus
25	chr13:92003800-92012200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr13:92003800-92012600	Weak transcription	Brain Hippocampus Middle	brain
27	chr13:92004000-92010800	Strong transcription	HUVEC	blood vessel
28	chr13:92004400-92010800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr13:92004600-92010800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr13:92004600-92011000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr13:92004600-92012200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr13:92004600-92021200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr13:92005200-92010800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr13:92005600-92011000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr13:92005800-92010800	Strong transcription	Primary T cells from cord blood	blood
36	chr13:92006000-92011000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr13:92006400-92010800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr13:92006600-92011000	Weak transcription	Brain Anterior Caudate	brain
39	chr13:92006600-92013400	Weak transcription	NHDF-Ad	bronchial
40	chr13:92007200-92011200	Strong transcription	GM12878-XiMat	blood
41	chr13:92007400-92011800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr13:92007600-92012200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr13:92007800-92012200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr13:92007800-92015200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr13:92008000-92011600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:92008400-92011400	Weak transcription	Placenta	Placenta
47	chr13:92008400-92011800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr13:92008400-92014600	Weak transcription	Hela-S3	cervix
49	chr13:92008600-92011400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr13:92008600-92014000	Weak transcription	Fetal Intestine Large	intestine

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