Variant report

Variant	rs55691643
Chromosome Location	chr8:100010709-100010710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:100009882-100010886	A549	lung:	n/a	chr8:100010278-100010296 chr8:100010285-100010293

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:100008104..100010992-chr8:100011648..100013634,2	MCF-7	breast:
2	chr8:99717734..99718483-chr8:100009688..100010929,4	MCF-7	breast:
3	chr8:99952900..99954204-chr8:100009550..100011340,25	MCF-7	breast:
4	chr8:99952911..99954006-chr8:100009839..100011083,7	MCF-7	breast:
5	chr8:99852770..99853592-chr8:100009889..100010836,2	MCF-7	breast:
6	chr8:99901892..99903288-chr8:100009594..100010716,5	MCF-7	breast:
7	chr8:100009588..100012990-chr8:100013654..100017766,5	K562	blood:
8	chr8:99952140..99962153-chr8:100006475..100015090,25	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS13B-1	chr8:100008217-100013862	NONHSAT127942

No data

Variant related genes	Relation type
ENSG00000263842	TF binding region
ENSG00000164920	Chromatin interaction
ENSG00000253180	Chromatin interaction
ENSG00000271930	Chromatin interaction
ENSG00000104375	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10087533	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10088152	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10091793	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10092190	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10096925	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10098153	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10104826	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10106041	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10108567	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10109066	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10808363	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10955197	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10955202	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11786078	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12547301	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12547849	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12550128	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12680054	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13256012	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13277925	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28886569	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2922070	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3019296	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34211616	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34836224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35018432	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4131359	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4133425	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4236854	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4260868	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4307310	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4317539	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4319053	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4327836	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4394363	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4428646	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4455798	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4461878	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4481561	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4489303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4520132	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4552872	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4734421	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4735603	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4735604	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4735607	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55837765	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55871624	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56315283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60950457	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60967421	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6415433	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6468647	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6468659	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6468663	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6468665	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6468669	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6468671	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6468675	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6989201	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6990741	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6991283	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6991585	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6992480	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6993878	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6997225	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7006391	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7007494	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7011648	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7011936	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7016044	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7016304	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7017261	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72668476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72668483	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72670294	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72670297	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72670301	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72672309	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72672313	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7341605	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7460376	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7461275	0.86[AMR][1000 genomes]
rs7462457	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7815414	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7818051	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7835084	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7836899	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7842393	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9297289	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9642956	0.84[ASN][1000 genomes]
rs9642958	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1023227	chr8:99902615-100290948	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv539692	chr8:99902615-100290948	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv1803951	chr8:99922754-100191783	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv611809	chr8:99925628-100093510	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv531505	chr8:99932947-100464147	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv1020174	chr8:99978271-100168938	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv539693	chr8:99978271-100168938	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55691643	ARHGEF12	trans	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99987200-100024200	Weak transcription	Osteobl	bone
2	chr8:100003400-100023400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr8:100006600-100024000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:100007000-100011400	Weak transcription	Fetal Heart	heart
5	chr8:100007000-100023800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:100007000-100024200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:100007200-100016000	Weak transcription	HSMMtube	muscle
8	chr8:100007200-100023000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr8:100007200-100023600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr8:100007200-100024000	Weak transcription	Ovary	ovary
11	chr8:100007200-100024400	Weak transcription	Aorta	Aorta
12	chr8:100007400-100014800	Weak transcription	Adipose Nuclei	Adipose
13	chr8:100007400-100015800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr8:100007800-100018200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:100008200-100018000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr8:100008600-100021800	Weak transcription	NHDF-Ad	bronchial
17	chr8:100008600-100024000	Weak transcription	NHLF	lung
18	chr8:100008800-100022400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links