Variant report

Variant	rs7318578
Chromosome Location	chr13:92005469-92005470
allele	A/C
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:15)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:92004231..92005934-chr9:134000945..134002528,2	K562	blood:
2	chr13:92004480..92006779-chr13:92126847..92129615,2	K562	blood:
3	chr13:92004766..92010130-chr13:92235897..92240121,6	K562	blood:
4	chr13:91810897..91813818-chr13:92005189..92006856,2	K562	blood:
5	chr13:92004916..92007687-chr14:39637524..39640281,2	K562	blood:
6	chr13:92005453..92007764-chr13:92312493..92314685,2	K562	blood:
7	chr13:92004766..92008845-chr13:92235897..92239237,4	K562	blood:
8	chr13:92004950..92005503-chr21:46961860..46962391,2	NB4	blood:
9	chr11:65190238..65193171-chr13:92003562..92006013,2	K562	blood:
10	chr13:91833346..91836233-chr13:92004886..92007249,2	K562	blood:
11	chr13:91867306..91869481-chr13:92003803..92007635,3	K562	blood:
12	chr1:244996766..244998804-chr13:92005393..92008126,2	K562	blood:
13	chr13:91925284..91927675-chr13:92003883..92005533,2	K562	blood:
14	chr13:92004230..92006612-chr6:18154943..18157881,2	K562	blood:
15	chr13:92004278..92006382-chr5:27545617..27547117,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPC5-1	chr13:92001952-92006829	NONHSAT034665

No data

Variant related genes	Relation type
ENSG00000182400	Chromatin interaction
ENSG00000203667	Chromatin interaction
ENSG00000165097	Chromatin interaction
ENSG00000173638	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000126883	Chromatin interaction
ENSG00000137364	Chromatin interaction
ENSG00000252622	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1324062	0.88[CHD][hapmap]
rs1428	0.83[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs2224851	0.85[CHD][hapmap]
rs2351704	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7322083	0.85[CHD][hapmap]
rs7995597	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7995682	0.85[LWK][hapmap];0.89[MKK][hapmap]
rs8000928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9523328	0.85[CHD][hapmap]

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
rs7318578	TRPM7	trans	cerebellum	SCAN
rs7318578	GPC5	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92001400-92005800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
2	chr13:92001600-92010200	Weak transcription	Spleen	Spleen
3	chr13:92001600-92010800	Weak transcription	Pancreas	Pancrea
4	chr13:92001600-92012200	Weak transcription	Esophagus	oesophagus
5	chr13:92001800-92007000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:92001800-92015600	Weak transcription	Ovary	ovary
7	chr13:92001800-92027200	Weak transcription	Aorta	Aorta
8	chr13:92002000-92005800	Weak transcription	Stomach Mucosa	stomach
9	chr13:92002000-92008400	Strong transcription	Placenta	Placenta
10	chr13:92002000-92011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr13:92002000-92011200	Weak transcription	Colonic Mucosa	Colon
12	chr13:92002000-92012200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr13:92002200-92007200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
14	chr13:92002200-92008400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr13:92002200-92008800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:92002200-92010800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr13:92002400-92006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr13:92002400-92010800	Weak transcription	Brain Angular Gyrus	brain
19	chr13:92002400-92012000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr13:92002600-92005600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr13:92002600-92005800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr13:92002800-92009600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr13:92002800-92009800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr13:92002800-92010000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr13:92003000-92008000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr13:92003000-92009000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr13:92003000-92009000	Weak transcription	Lung	lung
28	chr13:92003000-92009400	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr13:92003200-92010400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr13:92003400-92010000	Weak transcription	Fetal Brain Male	brain
31	chr13:92003400-92014000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr13:92003600-92005600	Weak transcription	Brain Anterior Caudate	brain
33	chr13:92003600-92005600	Weak transcription	Fetal Kidney	kidney
34	chr13:92003600-92006000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr13:92003600-92006000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr13:92003600-92006000	Weak transcription	Fetal Intestine Small	intestine
37	chr13:92003600-92006200	Weak transcription	Primary B cells from cord blood	blood
38	chr13:92003600-92006200	Weak transcription	NHLF	lung
39	chr13:92003600-92006600	Enhancers	Fetal Heart	heart
40	chr13:92003600-92006600	Weak transcription	Fetal Stomach	stomach
41	chr13:92003600-92007200	Genic enhancers	HepG2	liver
42	chr13:92003600-92007400	Weak transcription	Left Ventricle	heart
43	chr13:92003600-92008000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:92003600-92008200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr13:92003600-92008400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr13:92003600-92008400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr13:92003600-92008800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr13:92003600-92009000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr13:92003600-92009200	Genic enhancers	Liver	Liver
50	chr13:92003600-92009200	Weak transcription	Brain Germinal Matrix	brain

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