Variant report

Variant	rs12650288
Chromosome Location	chr4:57335294-57335295
allele	A/G
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	chr4:57334621..57337468-chr4:57366931..57368856,2	K562	blood:
2	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
3	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
4	chr4:57334099..57335760-chr4:57411009..57413881,2	K562	blood:
5	chr4:57300392..57305074-chr4:57333261..57337861,17	MCF-7	breast:
6	chr4:57333087..57335313-chr4:57842375..57845002,3	K562	blood:
7	chr4:57332287..57335313-chr4:57842375..57846822,5	K562	blood:
8	chr4:57333435..57335762-chr4:57336689..57342030,5	MCF-7	breast:
9	chr4:57334260..57336507-chr4:57410772..57412509,2	K562	blood:
10	chr4:57252130..57255932-chr4:57332416..57336369,6	K562	blood:
11	chr4:57333899..57336357-chr4:57340358..57342235,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000084092	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000047315	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1140982	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1142851	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934479	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11940993	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640212	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12643989	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12643996	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12644498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12649799	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13134963	0.83[JPT][hapmap]
rs1579019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086759	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17086773	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17086801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086830	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086860	0.83[YRI][hapmap]
rs17086868	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086898	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086909	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086919	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086922	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001807	0.82[YRI][hapmap]
rs2176785	0.83[JPT][hapmap]
rs2271924	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34398021	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34419325	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733324	1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs3733326	0.85[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796539	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796540	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796549	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796550	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4076103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128534	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs41498446	0.85[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs4631106	0.83[JPT][hapmap]
rs55778537	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55890437	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55903333	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55909588	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56129706	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56296497	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56362514	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57245446	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58654038	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59153415	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59686671	0.84[EUR][1000 genomes]
rs59764923	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59828502	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830145	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6831869	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7437839	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7658340	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7688482	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12650288	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57331800-57335600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr4:57332000-57335800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr4:57332200-57335800	Active TSS	K562	blood
4	chr4:57332400-57335400	Active TSS	A549	lung
5	chr4:57332400-57335400	Active TSS	NHLF	lung
6	chr4:57332400-57335800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:57332400-57335800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr4:57332600-57335400	Active TSS	HSMM	muscle
9	chr4:57334000-57335400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr4:57334000-57335600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr4:57334200-57335400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr4:57334200-57336000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:57334200-57336400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:57334400-57335600	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr4:57334400-57335800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:57334400-57335800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:57334400-57336200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:57334400-57336200	Flanking Active TSS	HUVEC	blood vessel
19	chr4:57334600-57335400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr4:57334600-57335400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:57334600-57335400	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr4:57334600-57335400	Active TSS	HepG2	liver
23	chr4:57334600-57335600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:57334600-57335600	Flanking Active TSS	NH-A	brain
25	chr4:57334600-57335600	Flanking Active TSS	Osteobl	bone
26	chr4:57334600-57335800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:57334600-57335800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:57334600-57335800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr4:57334600-57335800	Flanking Active TSS	Dnd41	blood
30	chr4:57334600-57336000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr4:57334800-57335400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr4:57334800-57335600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr4:57334800-57335600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr4:57334800-57335600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr4:57334800-57335600	Enhancers	Brain Cingulate Gyrus	brain
36	chr4:57334800-57335600	Enhancers	Colon Smooth Muscle	Colon
37	chr4:57334800-57335600	Flanking Active TSS	NHEK	skin
38	chr4:57334800-57336000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:57334800-57336000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:57334800-57336200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:57334800-57336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:57334800-57336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:57334800-57336400	Enhancers	Primary B cells from peripheral blood	blood
44	chr4:57334800-57336400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr4:57334800-57336400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:57334800-57336400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr4:57334800-57336600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr4:57334800-57336600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr4:57334800-57337800	Weak transcription	Esophagus	oesophagus
50	chr4:57334800-57337800	Weak transcription	Gastric	stomach

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