Variant report

Variant	rs2542588
Chromosome Location	chr2:54018924-54018925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54012419..54016440-chr2:54016510..54019549,4	K562	blood:
2	chr2:54018818..54021003-chr2:54021378..54023244,2	K562	blood:

Variant related genes	Relation type
ENSG00000115239	Chromatin interaction
ENSG00000068912	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10171954	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10178643	0.90[ASN][1000 genomes]
rs10188142	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10192626	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10201938	0.90[ASN][1000 genomes]
rs10203095	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10490471	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11684084	0.85[ASN][1000 genomes]
rs12621225	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs13414216	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13417926	0.85[ASN][1000 genomes]
rs13432632	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2111622	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2111623	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2160929	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2160931	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2193682	0.80[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2193683	0.85[ASN][1000 genomes]
rs2253760	0.86[YRI][hapmap];0.89[AFR][1000 genomes]
rs2357693	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2542571	0.93[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs2542574	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542575	0.84[AFR][1000 genomes]
rs2542576	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2542577	0.84[AFR][1000 genomes]
rs2542579	0.90[ASN][1000 genomes]
rs2542584	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542585	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542593	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2692514	0.95[LWK][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs2692515	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692518	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692531	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692532	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692537	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2909263	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2949811	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2949812	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770403	0.82[ASN][1000 genomes]
rs3821081	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4413193	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4671529	0.94[ASN][1000 genomes]
rs4671583	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs56173218	0.88[ASN][1000 genomes]
rs62139835	0.80[ASN][1000 genomes]
rs6705712	0.91[CHB][hapmap];0.92[CHD][hapmap];0.88[ASN][1000 genomes]
rs6708095	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6738369	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6743627	0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap];0.82[ASN][1000 genomes]
rs698854	0.92[ASN][1000 genomes]
rs7556791	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs7557799	0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7557898	0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs7569214	0.83[MEX][hapmap]
rs7572776	0.92[ASN][1000 genomes]
rs7573991	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7584474	0.80[ASN][1000 genomes]
rs7596349	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7601692	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs805322	0.81[TSI][hapmap]
rs805373	0.84[GIH][hapmap]
rs805374	0.88[GIH][hapmap]
rs805375	0.90[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs805410	0.83[GIH][hapmap]
rs805423	0.81[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs805433	0.88[ASN][1000 genomes]
rs805436	0.90[ASN][1000 genomes]
rs805438	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs805439	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs805441	0.83[ASN][1000 genomes]
rs805450	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs918207	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2542588	PSME4	cis	lymphoblastoid	seeQTL
rs2542588	ACYP2	cis	multi-tissue	Pritchard
rs2542588	PRDXDD1P	cis	parietal	SCAN
rs2542588	ACYP2	cis	Muscle Skeletal	GTEx
rs2542588	ACYP2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54024000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54015200-54025400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:54015200-54029800	Weak transcription	Esophagus	oesophagus
4	chr2:54015200-54038200	Weak transcription	Small Intestine	intestine
5	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
7	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
8	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:54015400-54021600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:54015600-54020000	Weak transcription	Brain Angular Gyrus	brain
11	chr2:54015600-54021600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:54015600-54022000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:54015600-54022200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:54015600-54022200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:54015600-54022200	Weak transcription	Brain Germinal Matrix	brain
16	chr2:54015600-54022200	Weak transcription	Fetal Kidney	kidney
17	chr2:54015600-54022800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:54015600-54029600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:54015600-54035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:54015600-54035800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:54015800-54019400	Weak transcription	Fetal Lung	lung
23	chr2:54015800-54019400	Weak transcription	Fetal Stomach	stomach
24	chr2:54015800-54019400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:54015800-54019600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:54015800-54019600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:54015800-54019600	Weak transcription	NHLF	lung
28	chr2:54015800-54019800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:54015800-54019800	Weak transcription	Colonic Mucosa	Colon
30	chr2:54015800-54021000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:54015800-54021000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:54015800-54021000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:54015800-54021000	Weak transcription	HSMM	muscle
34	chr2:54015800-54021000	Weak transcription	NHDF-Ad	bronchial
35	chr2:54015800-54021200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:54015800-54021200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr2:54015800-54021200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:54015800-54021200	Weak transcription	Placenta	Placenta
39	chr2:54015800-54021400	Weak transcription	Fetal Thymus	thymus
40	chr2:54015800-54021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:54015800-54022000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:54015800-54022000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:54015800-54022000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:54015800-54022000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:54015800-54022000	Weak transcription	Adipose Nuclei	Adipose
46	chr2:54015800-54022000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:54015800-54022000	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:54015800-54022000	Weak transcription	NH-A	brain
49	chr2:54015800-54022200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:54015800-54022200	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links