Variant report

Variant	rs2542574
Chromosome Location	chr2:54047432-54047433
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	chr15:50646356..50648694-chr2:54046966..54049635,2	MCF-7	breast:
2	chr2:54043746..54045589-chr2:54047381..54048993,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10171954	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10178643	0.84[ASN][1000 genomes]
rs10188142	0.86[ASN][1000 genomes]
rs10192626	0.88[ASN][1000 genomes]
rs10201938	0.85[ASN][1000 genomes]
rs10203095	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10490471	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11684084	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12621225	0.80[ASN][1000 genomes]
rs13414216	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13417926	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13432632	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2111622	0.86[ASN][1000 genomes]
rs2111623	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2160931	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2193682	0.80[EUR][1000 genomes]
rs2193683	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2357693	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2542576	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2542579	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542584	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542585	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542588	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542593	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692515	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2692518	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692531	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2692532	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2692536	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2692537	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2909263	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2949811	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2949812	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770403	0.83[EUR][1000 genomes]
rs3770405	0.81[EUR][1000 genomes]
rs3821081	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4413193	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671529	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671583	0.88[ASN][1000 genomes]
rs56173218	0.83[ASN][1000 genomes]
rs6705712	0.82[ASN][1000 genomes]
rs6708095	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6738369	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698854	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718872	0.80[EUR][1000 genomes]
rs7572776	0.86[ASN][1000 genomes]
rs7573991	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7596349	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7601692	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs805322	0.89[EUR][1000 genomes]
rs805359	0.87[EUR][1000 genomes]
rs805374	0.89[EUR][1000 genomes]
rs805375	0.89[EUR][1000 genomes]
rs805379	0.90[EUR][1000 genomes]
rs805380	0.88[EUR][1000 genomes]
rs805391	0.86[EUR][1000 genomes]
rs805392	0.88[EUR][1000 genomes]
rs805393	0.85[EUR][1000 genomes]
rs805402	0.86[EUR][1000 genomes]
rs805405	0.86[EUR][1000 genomes]
rs805410	0.88[EUR][1000 genomes]
rs805421	0.85[EUR][1000 genomes]
rs805423	0.90[EUR][1000 genomes]
rs805424	0.88[EUR][1000 genomes]
rs805430	0.88[EUR][1000 genomes]
rs805433	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs805436	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805438	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs805439	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs805441	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs805450	0.80[EUR][1000 genomes]
rs809280	0.90[EUR][1000 genomes]
rs918207	0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2542574	ACYP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
2	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:54020600-54048400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:54020600-54048600	Strong transcription	Osteobl	bone
7	chr2:54021000-54048000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:54021200-54047600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:54021800-54047600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:54022000-54047600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
13	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
15	chr2:54035800-54052800	Weak transcription	Brain Substantia Nigra	brain
16	chr2:54038800-54053000	Weak transcription	Fetal Brain Male	brain
17	chr2:54040200-54055000	Weak transcription	Fetal Heart	heart
18	chr2:54040600-54053000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:54040800-54048000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:54040800-54053000	Weak transcription	Brain Angular Gyrus	brain
21	chr2:54040800-54053000	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:54041400-54049200	Weak transcription	K562	blood
23	chr2:54041400-54054600	Weak transcription	Psoas Muscle	Psoas
24	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:54042200-54047600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:54042400-54048200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr2:54042800-54047800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:54042800-54062200	Weak transcription	Fetal Kidney	kidney
29	chr2:54043000-54053800	Weak transcription	NHEK	skin
30	chr2:54043200-54053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:54043200-54053800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:54043400-54053000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:54043400-54053600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:54044600-54048800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:54045400-54047800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:54045400-54053000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:54045400-54053000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:54045600-54047600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:54046000-54053600	Weak transcription	NH-A	brain
40	chr2:54046200-54047600	Strong transcription	Colon Smooth Muscle	Colon
41	chr2:54046200-54050200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:54046200-54050600	Strong transcription	Fetal Stomach	stomach
43	chr2:54046400-54053000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:54046600-54049000	Weak transcription	Hela-S3	cervix
45	chr2:54046600-54049800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
48	chr2:54046800-54047800	Enhancers	Duodenum Mucosa	Duodenum
49	chr2:54046800-54048200	Enhancers	Fetal Intestine Small	intestine
50	chr2:54046800-54048400	Strong transcription	GM12878-XiMat	blood

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