Variant report

Variant	rs12458598
Chromosome Location	chr18:13238715-13238716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13237575..13239719-chr18:13241059..13243082,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12607576	0.91[CHD][hapmap];0.83[GIH][hapmap]
rs12955200	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12968182	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12968748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3901403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4277409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4616353	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4797744	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4797747	0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4797749	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4797750	0.89[CEU][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4797752	0.80[MEX][hapmap]
rs59835474	0.81[ASN][1000 genomes]
rs6505789	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67772629	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7228009	0.81[EUR][1000 genomes]
rs7244519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944928	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9952107	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9952186	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9952516	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9952649	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9955376	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9955747	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9958724	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9962328	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9967502	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv909409	chr18:13151544-13240284	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv909410	chr18:13151544-13308950	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12458598	PSMG2	cis	lymphoblastoid	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13223600-13241400	Weak transcription	Aorta	Aorta
2	chr18:13223800-13259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr18:13224000-13259800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr18:13224400-13242600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr18:13224400-13245400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr18:13224400-13259800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr18:13229400-13243000	Weak transcription	Dnd41	blood
8	chr18:13230600-13240800	Enhancers	Fetal Brain Male	brain
9	chr18:13232800-13246200	Weak transcription	Psoas Muscle	Psoas
10	chr18:13233000-13239600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr18:13233000-13241400	Enhancers	Fetal Brain Female	brain
12	chr18:13233000-13260200	Weak transcription	Colonic Mucosa	Colon
13	chr18:13233200-13240600	Enhancers	Brain Anterior Caudate	brain
14	chr18:13233200-13245800	Weak transcription	Right Atrium	heart
15	chr18:13233400-13239600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr18:13233400-13254000	Weak transcription	Spleen	Spleen
17	chr18:13233400-13259000	Weak transcription	Primary T cells from cord blood	blood
18	chr18:13233600-13243000	Weak transcription	Gastric	stomach
19	chr18:13234800-13239200	Weak transcription	Liver	Liver
20	chr18:13234800-13239400	Weak transcription	Thymus	Thymus
21	chr18:13234800-13239400	Weak transcription	HepG2	liver
22	chr18:13234800-13240200	Weak transcription	Pancreas	Pancrea
23	chr18:13235600-13240600	Enhancers	Brain Hippocampus Middle	brain
24	chr18:13235800-13239400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr18:13235800-13245800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr18:13236000-13239400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr18:13236000-13239600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr18:13236000-13241200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr18:13236200-13258800	Weak transcription	Fetal Lung	lung
30	chr18:13236600-13239200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr18:13236800-13240800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr18:13237000-13239600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr18:13237000-13240200	Enhancers	Brain Substantia Nigra	brain
34	chr18:13237000-13240200	Weak transcription	Fetal Thymus	thymus
35	chr18:13237400-13239200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr18:13237400-13239600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr18:13237400-13240400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr18:13237400-13258800	Weak transcription	Adipose Nuclei	Adipose
39	chr18:13237400-13258800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr18:13237800-13239200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr18:13237800-13258800	Weak transcription	Colon Smooth Muscle	Colon
42	chr18:13238000-13239600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr18:13238200-13239600	Weak transcription	Left Ventricle	heart
44	chr18:13238400-13238800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr18:13238600-13238800	Enhancers	Fetal Muscle Trunk	muscle
46	chr18:13238600-13239200	Weak transcription	Brain Angular Gyrus	brain
47	chr18:13238600-13239600	Weak transcription	Right Ventricle	heart
48	chr18:13238600-13240400	Enhancers	Brain Germinal Matrix	brain
49	chr18:13238600-13245200	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links