Variant report

Variant	rs2542577
Chromosome Location	chr2:54049248-54049249
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:

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17039525	0.84[ASN][1000 genomes]
rs17045199	0.84[ASN][1000 genomes]
rs2253760	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542571	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2542575	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542588	0.84[AFR][1000 genomes]
rs2692514	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692516	0.93[ASN][1000 genomes]
rs2692534	0.86[ASN][1000 genomes]
rs2909261	0.95[ASN][1000 genomes]
rs3095756	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35487539	0.85[ASN][1000 genomes]
rs58359565	0.85[ASN][1000 genomes]
rs698853	0.94[ASN][1000 genomes]
rs7583622	0.85[ASN][1000 genomes]
rs805376	0.80[ASN][1000 genomes]
rs805377	0.80[ASN][1000 genomes]
rs805416	0.90[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2542577	PSME4	Cis_1M	lymphoblastoid	RTeQTL
rs2542577	ACYP2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:106 , 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	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
7	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
9	chr2:54035800-54052800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:54038800-54053000	Weak transcription	Fetal Brain Male	brain
11	chr2:54040200-54055000	Weak transcription	Fetal Heart	heart
12	chr2:54040600-54053000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:54040800-54053000	Weak transcription	Brain Angular Gyrus	brain
14	chr2:54040800-54053000	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:54041400-54054600	Weak transcription	Psoas Muscle	Psoas
16	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:54042800-54062200	Weak transcription	Fetal Kidney	kidney
18	chr2:54043000-54053800	Weak transcription	NHEK	skin
19	chr2:54043200-54053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:54043200-54053800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:54043400-54053000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:54043400-54053600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:54045400-54053000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:54045400-54053000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:54046000-54053600	Weak transcription	NH-A	brain
26	chr2:54046200-54050200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:54046200-54050600	Strong transcription	Fetal Stomach	stomach
28	chr2:54046400-54053000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:54046600-54049800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
32	chr2:54046800-54053000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:54046800-54054000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:54046800-54054200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:54046800-54054200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:54046800-54056800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:54046800-54060400	Weak transcription	Primary B cells from cord blood	blood
38	chr2:54046800-54070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:54046800-54080400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:54047000-54051200	Weak transcription	HUVEC	blood vessel
41	chr2:54047000-54053000	Weak transcription	Ovary	ovary
42	chr2:54047000-54053000	Weak transcription	HMEC	breast
43	chr2:54047000-54053800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:54047000-54054000	Weak transcription	NHLF	lung
45	chr2:54047000-54056600	Weak transcription	Brain Germinal Matrix	brain
46	chr2:54047000-54060600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr2:54047000-54061400	Weak transcription	Fetal Thymus	thymus
48	chr2:54047000-54080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:54047000-54080200	Weak transcription	A549	lung
50	chr2:54047000-54080400	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links