Variant report

Variant	rs308911
Chromosome Location	chr2:86855977-86855978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr2:86855725-86856159	HepG2	liver:	n/a	n/a
2	ARID3A	chr2:86855072-86856087	HepG2	liver:	n/a	n/a
3	MYBL2	chr2:86855063-86856116	HepG2	liver:	n/a	n/a
4	FOXA1	chr2:86855846-86856294	HepG2	liver:	n/a	n/a
5	RFX5	chr2:86855910-86856256	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:86855526..86858566-chr2:86929665..86933195,3	MCF-7	breast:
2	chr2:86849700..86853087-chr2:86854052..86858493,4	K562	blood:
3	chr2:86834891..86837645-chr2:86855817..86858466,2	MCF-7	breast:
4	chr2:86855492..86857596-chr2:86858665..86860258,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNF103	TF binding region
ENSG00000239305	Chromatin interaction
ENSG00000249884	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1036940	0.82[GIH][hapmap]
rs11127047	0.91[GIH][hapmap]
rs12623509	0.83[GIH][hapmap]
rs12714190	0.80[GIH][hapmap]
rs12995117	0.82[GIH][hapmap]
rs2044230	0.82[GIH][hapmap]
rs2120340	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218060	0.91[CEU][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs308901	0.95[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs308902	0.81[MEX][hapmap]
rs308903	0.81[MEX][hapmap]
rs308907	0.91[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs396354	0.85[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs433655	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs4832046	1.00[ASN][1000 genomes]
rs4832290	0.82[GIH][hapmap]
rs4832294	0.82[GIH][hapmap]
rs6547700	0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs6714826	0.82[GIH][hapmap]
rs6752371	0.81[GIH][hapmap]
rs683139	0.85[CEU][hapmap];0.91[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7557796	0.91[GIH][hapmap]
rs7584882	0.81[GIH][hapmap]
rs7596717	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs308911	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs308911	POLR1A	cis	cerebellum	SCAN
rs308911	PTCD3	cis	cerebellum	SCAN
rs308911	C2orf68	cis	cerebellum	SCAN
rs308911	RNF103	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86851000-86856400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:86851000-86860400	Weak transcription	Lung	lung
3	chr2:86851200-86858400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:86851200-86860400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:86851600-86856800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:86851600-86858600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:86851600-86858600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:86851600-86858600	Weak transcription	HMEC	breast
9	chr2:86851800-86860000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:86851800-86860400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:86852400-86858600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:86852600-86858600	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:86852800-86857200	Weak transcription	Colonic Mucosa	Colon
14	chr2:86852800-86859000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:86853000-86859000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:86853000-86859400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:86853000-86859600	Weak transcription	Brain Substantia Nigra	brain
18	chr2:86853000-86860400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:86853200-86860000	Weak transcription	Brain Anterior Caudate	brain
20	chr2:86854600-86856600	Enhancers	Duodenum Mucosa	Duodenum
21	chr2:86854600-86858000	Enhancers	Fetal Intestine Large	intestine
22	chr2:86854800-86856200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:86854800-86858400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr2:86855200-86856000	Flanking Active TSS	A549	lung
25	chr2:86855200-86856000	Flanking Active TSS	HepG2	liver
26	chr2:86855400-86856000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:86855400-86856200	Flanking Active TSS	Liver	Liver
28	chr2:86855400-86858400	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr2:86855600-86858600	Weak transcription	Gastric	stomach
30	chr2:86855600-86858600	Weak transcription	Pancreas	Pancrea
31	chr2:86855600-86858800	Weak transcription	Small Intestine	intestine
32	chr2:86855800-86856200	Weak transcription	Fetal Intestine Small	intestine
33	chr2:86855800-86856200	Weak transcription	Stomach Mucosa	stomach
34	chr2:86855800-86859000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links