Variant report

Variant	rs683139
Chromosome Location	chr2:86848185-86848186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86789208..86791396-chr2:86847374..86850220,3	K562	blood:
2	chr2:86788265..86792368-chr2:86847223..86851122,9	MCF-7	breast:
3	chr2:86416284..86418486-chr2:86847509..86849748,2	K562	blood:
4	chr2:86839004..86842325-chr2:86847581..86852030,6	MCF-7	breast:
5	chr2:86787885..86791617-chr2:86846945..86852237,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000228363	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10185085	0.87[CHD][hapmap]
rs1036940	0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs11127042	0.87[CHD][hapmap]
rs11127047	0.82[GIH][hapmap]
rs11693352	0.87[CHD][hapmap]
rs12714185	0.87[CHD][hapmap]
rs12714187	0.87[CHD][hapmap]
rs12995117	0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs2030259	0.87[CHD][hapmap]
rs2044230	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs2120340	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs218060	0.85[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2367575	0.80[ASN][1000 genomes]
rs308901	0.90[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs308902	0.81[MEX][hapmap]
rs308903	0.81[MEX][hapmap]
rs308907	0.85[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs308911	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]
rs396354	0.84[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs433655	1.00[CHD][hapmap];0.84[MEX][hapmap]
rs4832289	0.87[CHD][hapmap]
rs4832290	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs4832293	0.80[ASN][1000 genomes]
rs4832294	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs4832298	0.92[ASN][1000 genomes]
rs6547700	1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs6714826	0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs6714957	1.00[ASN][1000 genomes]
rs7557796	0.82[GIH][hapmap]
rs7574389	0.87[CHD][hapmap]
rs966477	0.87[CHD][hapmap];0.80[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs683139	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:86829400-86848400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:86829400-86849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:86829800-86849400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:86830000-86848600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:86830400-86848600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:86831800-86848200	Weak transcription	K562	blood
8	chr2:86832200-86848200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:86832400-86849400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:86832600-86848200	Weak transcription	Colonic Mucosa	Colon
11	chr2:86833000-86848200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:86836600-86848600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:86837000-86848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:86841200-86849600	Weak transcription	Gastric	stomach
15	chr2:86841200-86849600	Weak transcription	Spleen	Spleen
16	chr2:86841400-86849600	Weak transcription	Lung	lung
17	chr2:86842200-86849600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:86843000-86848200	Weak transcription	Aorta	Aorta
19	chr2:86843000-86849600	Weak transcription	Esophagus	oesophagus
20	chr2:86843200-86848200	Weak transcription	Psoas Muscle	Psoas
21	chr2:86843200-86849600	Weak transcription	Pancreas	Pancrea
22	chr2:86843400-86848200	Weak transcription	Thymus	Thymus
23	chr2:86844000-86848400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:86844200-86848600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:86845200-86848200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:86845200-86849600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:86845800-86848200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:86846200-86848200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:86846400-86848200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:86846400-86848400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:86846400-86848600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr2:86846600-86848200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:86846600-86848200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:86846600-86848200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:86846600-86848200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:86846600-86848200	Weak transcription	Ovary	ovary
37	chr2:86846600-86848200	Weak transcription	NH-A	brain
38	chr2:86846600-86848400	Weak transcription	Fetal Kidney	kidney
39	chr2:86846600-86848400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:86846800-86848400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:86846800-86848400	Weak transcription	Fetal Thymus	thymus
42	chr2:86847000-86848200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:86847200-86848600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr2:86847200-86848600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr2:86847200-86848800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:86847200-86851200	Active TSS	Duodenum Mucosa	Duodenum
47	chr2:86847200-86851400	Active TSS	Right Atrium	heart
48	chr2:86847400-86848200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:86847400-86848200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:86847400-86848200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links