Variant report

Variant	rs7718593
Chromosome Location	chr5:95988492-95988493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95982894..95985844-chr5:95986836..95989729,2	MCF-7	breast:
2	chr5:95987202..95990491-chr5:95996534..96000051,5	MCF-7	breast:
3	chr5:95976037..95979831-chr5:95983868..95989174,6	MCF-7	breast:
4	chr5:95987307..95988959-chr5:96004331..96007033,2	K562	blood:
5	chr5:95975136..95978102-chr5:95987198..95988940,2	MCF-7	breast:
6	chr5:95985902..95988959-chr5:96004331..96007887,4	K562	blood:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1037683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12514686	0.92[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap]
rs12518441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17086521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17086550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17086596	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17086611	1.00[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs6862241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7702304	0.91[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7718593	CAST	cis	cerebellum	SCAN
rs7718593	MCTP1	cis	parietal	SCAN
rs7718593	CAST	cis	multi-tissue	Pritchard

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95982800-95989600	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr5:95983200-95994200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:95983800-95990800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:95984400-95989200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:95984800-95989400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr5:95984800-95991000	Weak transcription	Psoas Muscle	Psoas
7	chr5:95984800-95991400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:95985400-95992000	Weak transcription	Pancreas	Pancrea
9	chr5:95985600-95990200	Weak transcription	A549	lung
10	chr5:95986000-95990800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:95986000-95990800	Weak transcription	Osteobl	bone
12	chr5:95986000-95991000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:95986000-95991000	Weak transcription	Liver	Liver
14	chr5:95986200-95988600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:95986200-95990200	Weak transcription	HSMM	muscle
16	chr5:95986200-95990800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:95986200-95992000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:95986200-95992000	Weak transcription	Fetal Intestine Small	intestine
19	chr5:95986200-95992000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:95986400-95991000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:95986600-95991000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:95986600-95992000	Weak transcription	Fetal Intestine Large	intestine
23	chr5:95987400-95990800	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:95987600-95989400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr5:95987800-95989200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:95987800-95989400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr5:95988000-95988800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:95988000-95989000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr5:95988200-95988600	Enhancers	Esophagus	oesophagus
30	chr5:95988200-95988800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr5:95988200-95988800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr5:95988200-95988800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:95988200-95989000	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr5:95988200-95989000	Enhancers	NHLF	lung
35	chr5:95988200-95989200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:95988200-95989200	Enhancers	Placenta	Placenta
37	chr5:95988200-95989400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:95988200-95989400	Enhancers	HMEC	breast
39	chr5:95988200-95989600	Enhancers	Hela-S3	cervix
40	chr5:95988400-95988600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:95988400-95989000	Enhancers	Fetal Lung	lung
42	chr5:95988400-95989200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:95988400-95989200	Enhancers	Fetal Kidney	kidney
44	chr5:95988400-95989200	Enhancers	NHDF-Ad	bronchial
45	chr5:95988400-95989400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:95988400-95989400	Enhancers	NH-A	brain
47	chr5:95988400-95994600	Enhancers	NHEK	skin

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