Variant report

Variant	rs718936
Chromosome Location	chr2:172863743-172863744
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172863381..172865132-chr2:172924958..172927915,2	MCF-7	breast:
2	chr2:172863226..172865802-chr2:172966081..172969208,5	MCF-7	breast:
3	chr2:172860607..172867322-chr2:172946572..172954768,24	MCF-7	breast:
4	chr2:172863189..172867097-chr2:172945137..172953576,15	K562	blood:
5	chr2:172824373..172826532-chr2:172862535..172864466,2	K562	blood:
6	chr2:172777448..172780686-chr2:172863264..172866650,5	K562	blood:
7	chr2:172859788..172868192-chr2:172944876..172951443,18	MCF-7	breast:
8	chr2:172861569..172867068-chr2:172965912..172971063,13	K562	blood:
9	chr2:172863189..172870519-chr2:172946500..172952655,22	K562	blood:
10	chr2:172749212..172752099-chr2:172863500..172865923,3	MCF-7	breast:
11	chr2:172862808..172868920-chr2:172961807..172971063,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236651	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000128708	Chromatin interaction
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10177679	1.00[CEU][hapmap]
rs10196521	1.00[CEU][hapmap]
rs10930497	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11676484	1.00[CEU][hapmap]
rs12473516	1.00[MEX][hapmap]
rs12473876	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12479374	1.00[CEU][hapmap]
rs12988626	1.00[ASN][1000 genomes]
rs1400816	1.00[CEU][hapmap]
rs17581715	1.00[CEU][hapmap]
rs1878583	1.00[CEU][hapmap]
rs1982288	1.00[CEU][hapmap]
rs2028670	1.00[CEU][hapmap]
rs2028671	1.00[CEU][hapmap]
rs2028672	1.00[CEU][hapmap]
rs2357208	1.00[CEU][hapmap]
rs28372952	1.00[CEU][hapmap]
rs34535766	1.00[ASN][1000 genomes]
rs3770443	1.00[CEU][hapmap]
rs3791343	1.00[AFR][1000 genomes]
rs3821092	1.00[CEU][hapmap]
rs3821094	1.00[CEU][hapmap]
rs3821096	1.00[CEU][hapmap]
rs4668417	1.00[CEU][hapmap]
rs6433315	1.00[CEU][hapmap]
rs6433318	1.00[CEU][hapmap]
rs6433322	1.00[CEU][hapmap]
rs66536067	1.00[ASN][1000 genomes]
rs6707142	1.00[CEU][hapmap]
rs6714214	1.00[CEU][hapmap]
rs6733525	1.00[ASN][1000 genomes]
rs6753859	1.00[CEU][hapmap]
rs7560031	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579509	0.82[CEU][hapmap]
rs7580132	0.82[CEU][hapmap]
rs7607377	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs718936	FGD5	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172847400-172864000	Weak transcription	HSMM	muscle
2	chr2:172849600-172863800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:172861200-172864000	Weak transcription	Right Atrium	heart
4	chr2:172861200-172864200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:172861400-172863800	Weak transcription	Ovary	ovary
6	chr2:172861400-172864000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:172862200-172863800	Weak transcription	Fetal Brain Male	brain
8	chr2:172862200-172863800	Enhancers	NHEK	skin
9	chr2:172862800-172864000	Active TSS	Brain Angular Gyrus	brain
10	chr2:172863000-172864000	Weak transcription	Esophagus	oesophagus
11	chr2:172863200-172863800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:172863200-172863800	Enhancers	K562	blood
13	chr2:172863200-172864000	Active TSS	Brain Cingulate Gyrus	brain
14	chr2:172863400-172863800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:172863600-172863800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:172863600-172863800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:172863600-172863800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:172863600-172863800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr2:172863600-172863800	Bivalent Enhancer	Fetal Kidney	kidney
20	chr2:172863600-172863800	Enhancers	Dnd41	blood
21	chr2:172863600-172863800	Enhancers	Hela-S3	cervix
22	chr2:172863600-172863800	Enhancers	HepG2	liver
23	chr2:172863600-172864000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:172863600-172864000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:172863600-172864000	Enhancers	GM12878-XiMat	blood
26	chr2:172863600-172864000	Enhancers	HMEC	breast
27	chr2:172863600-172864600	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr2:172863600-172865600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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