Variant report

Variant	rs2692534
Chromosome Location	chr2:54011379-54011380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr2:54011285-54011485	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54006024..54008035-chr2:54009628..54012351,2	K562	blood:
2	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:

Variant related genes	Relation type
ERLEC1	TF binding region
ENSG00000143942	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10183655	0.83[CHB][hapmap]
rs10490468	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs17039525	0.91[ASN][1000 genomes]
rs17045199	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17045452	0.84[CEU][hapmap];0.87[CHB][hapmap]
rs2009144	0.80[ASN][1000 genomes]
rs2253760	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2542571	0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2542575	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs2542577	0.86[ASN][1000 genomes]
rs2542582	0.92[CEU][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes]
rs2542583	0.82[AMR][1000 genomes]
rs2542589	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs2542590	0.82[AMR][1000 genomes]
rs2542591	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs2542592	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs2692512	0.83[AMR][1000 genomes]
rs2692513	0.82[AMR][1000 genomes]
rs2692514	0.81[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2692516	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2692519	0.92[CEU][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes]
rs2692522	0.82[AMR][1000 genomes]
rs2692530	0.81[AMR][1000 genomes]
rs2692533	0.92[CEU][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs2909261	0.82[ASN][1000 genomes]
rs2909262	0.82[AMR][1000 genomes]
rs2909459	0.87[CHB][hapmap]
rs3095756	0.86[ASN][1000 genomes]
rs35487539	0.91[ASN][1000 genomes]
rs3731967	0.83[CHB][hapmap]
rs3731970	0.83[ASN][1000 genomes]
rs3770407	0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs3770408	0.82[ASN][1000 genomes]
rs3770409	0.82[ASN][1000 genomes]
rs58359565	0.92[ASN][1000 genomes]
rs62137566	0.85[ASN][1000 genomes]
rs698853	0.85[ASN][1000 genomes]
rs698855	0.80[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs72901242	0.80[ASN][1000 genomes]
rs7583622	0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs766075	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs805310	0.84[CEU][hapmap];0.87[CHB][hapmap]
rs805321	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs805328	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs805334	0.86[CEU][hapmap]
rs805351	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs805352	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]
rs805365	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]
rs805386	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs805399	0.95[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs805401	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs805404	0.80[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs805408	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs805426	0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap]
rs805437	0.84[CEU][hapmap];0.81[LWK][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2692534	ACYP2	cis	Muscle Skeletal	GTEx
rs2692534	ACYP2	cis	multi-tissue	Pritchard
rs2692534	MTIF2	cis	cerebellum	SCAN
rs2692534	PSME4	cis	lymphoblastoid	seeQTL
rs2692534	PSME4	Cis_1M	lymphoblastoid	RTeQTL
rs2692534	PRDXDD1P	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53995600-54011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:53995600-54011400	Weak transcription	Right Atrium	heart
3	chr2:53995600-54011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:53995600-54012000	Weak transcription	Left Ventricle	heart
5	chr2:53995600-54012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:53995800-54011400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:53995800-54011600	Weak transcription	Psoas Muscle	Psoas
8	chr2:53995800-54011800	Weak transcription	Right Ventricle	heart
9	chr2:53995800-54012000	Weak transcription	Adipose Nuclei	Adipose
10	chr2:53995800-54012200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:53995800-54012400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:53995800-54012600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:53996000-54011600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:53996000-54011600	Weak transcription	Fetal Lung	lung
15	chr2:53996000-54011800	Weak transcription	NHDF-Ad	bronchial
16	chr2:53996200-54011400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:53996200-54012600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:53996400-54011400	Weak transcription	Thymus	Thymus
19	chr2:53996400-54011600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:53996400-54011800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:53996400-54011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:53996400-54012200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:53996400-54012400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:53996600-54011400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:53997000-54011400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:53997000-54011600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:54002800-54011400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:54003400-54011400	Weak transcription	Fetal Heart	heart
29	chr2:54004000-54012600	Weak transcription	Small Intestine	intestine
30	chr2:54004200-54012200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:54004600-54012600	Weak transcription	HSMMtube	muscle
32	chr2:54004600-54013200	Weak transcription	Aorta	Aorta
33	chr2:54006200-54012000	Weak transcription	HUVEC	blood vessel
34	chr2:54007400-54011600	Weak transcription	A549	lung
35	chr2:54007600-54011600	Weak transcription	NH-A	brain
36	chr2:54007800-54011400	Weak transcription	Pancreas	Pancrea
37	chr2:54007800-54011400	Weak transcription	K562	blood
38	chr2:54007800-54011600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:54007800-54012000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:54008000-54011400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:54008000-54011400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:54008600-54012600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:54008600-54012800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:54008800-54011400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:54008800-54011600	Weak transcription	Spleen	Spleen
46	chr2:54009400-54011400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:54009400-54011800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:54009400-54012000	Weak transcription	Fetal Stomach	stomach
49	chr2:54009400-54012000	Weak transcription	Lung	lung
50	chr2:54009400-54012800	Weak transcription	Placenta	Placenta

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