Variant report

Variant	rs34498089
Chromosome Location	chr2:54308826-54308827
allele	A/G
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	JUND	chr2:54308731-54309253	K562	blood:	n/a	chr2:54308910-54308920 chr2:54308910-54308920 chr2:54308910-54308920 chr2:54308910-54308920
2	PAX5	chr2:54308513-54309149	GM12891	blood:	n/a	chr2:54308929-54308938
3	CTCF	chr2:54308820-54308970	SAEC	small airway:	n/a	n/a
4	EBF1	chr2:54308636-54309097	GM12878	blood:	n/a	n/a
5	SP1	chr2:54308547-54309231	GM12878	blood:	n/a	n/a
6	EP300	chr2:54308761-54309256	K562	blood:	n/a	n/a
7	EGR1	chr2:54308765-54309038	GM12878	blood:	n/a	n/a
8	ATF1	chr2:54308755-54309212	K562	blood:	n/a	n/a
9	MYC	chr2:54308619-54309080	MCF10A-Er-Src	breast:	n/a	n/a
10	EBF1	chr2:54308782-54309036	GM12878	blood:	n/a	n/a
11	CEBPB	chr2:54308509-54309337	GM12878	blood:	n/a	chr2:54309304-54309317
12	STAT3	chr2:54308647-54309239	GM12878	blood:	n/a	chr2:54309071-54309080 chr2:54309070-54309079
13	POU2F2	chr2:54308568-54309229	GM12891	blood:	n/a	n/a
14	PAX5	chr2:54308706-54308992	GM12892	blood:	n/a	chr2:54308929-54308938
15	STAT5A	chr2:54308629-54309145	GM12878	blood:	n/a	chr2:54309071-54309080 chr2:54309070-54309079
16	BHLHE40	chr2:54308623-54309223	GM12878	blood:	n/a	chr2:54309198-54309214
17	SP1	chr2:54308655-54309146	GM12878	blood:	n/a	n/a
18	MAFK	chr2:54308776-54309084	K562	blood:	n/a	chr2:54308909-54308919
19	PAX5	chr2:54308572-54309133	GM12878	blood:	n/a	chr2:54308929-54308938
20	EP300	chr2:54308543-54309223	GM12878	blood:	n/a	n/a
21	IRF4	chr2:54308596-54309194	GM12878	blood:	n/a	n/a
22	EBF1	chr2:54308597-54309145	GM12878	blood:	n/a	n/a
23	EGR1	chr2:54308774-54308993	GM12878	blood:	n/a	n/a
24	STAT1	chr2:54308719-54309262	GM12878	blood:	n/a	chr2:54309071-54309080 chr2:54309070-54309079
25	POLR2A	chr2:54308819-54309146	GM12878	blood:	n/a	n/a
26	MTA3	chr2:54308450-54309363	GM12878	blood:	n/a	n/a
27	YY1	chr2:54308779-54309124	GM12878	blood:	n/a	n/a
28	PAX5	chr2:54308793-54309091	GM12891	blood:	n/a	chr2:54308929-54308938
29	NFYB	chr2:54308646-54309225	GM12878	blood:	n/a	n/a
30	TCF3	chr2:54308555-54309137	GM12878	blood:	n/a	n/a
31	FOS	chr2:54308703-54309047	MCF10A-Er-Src	breast:	n/a	chr2:54308910-54308920 chr2:54308910-54308920 chr2:54308910-54308920 chr2:54308910-54308920
32	POLR2A	chr2:54308574-54309238	GM12892	blood:	n/a	n/a
33	FOS	chr2:54308609-54309221	MCF10A-Er-Src	breast:	n/a	chr2:54308910-54308920 chr2:54308910-54308920 chr2:54308910-54308920 chr2:54308910-54308920
34	MEF2C	chr2:54308631-54309207	GM12878	blood:	n/a	n/a
35	BCLAF1	chr2:54308385-54309255	GM12878	blood:	n/a	chr2:54308929-54308938 chr2:54309019-54309026
36	PML	chr2:54308623-54309103	GM12878	blood:	n/a	n/a
37	PAX5	chr2:54308597-54309259	GM12878	blood:	n/a	chr2:54308929-54308938
38	NR2F2	chr2:54308823-54309175	K562	blood:	n/a	n/a
39	MEF2A	chr2:54308580-54309117	GM12878	blood:	n/a	n/a
40	TCF12	chr2:54308584-54309116	GM12878	blood:	n/a	n/a
41	POU2F2	chr2:54308775-54309012	GM12878	blood:	n/a	n/a
42	POLR2A	chr2:54308762-54309148	K562	blood:	n/a	n/a
43	GATA2	chr2:54308714-54309248	K562	blood:	n/a	chr2:54308914-54308921
44	RCOR1	chr2:54308780-54309244	K562	blood:	n/a	n/a
45	CEBPB	chr2:54308671-54309130	GM12878	blood:	n/a	n/a
46	BCL11A	chr2:54308658-54309115	GM12878	blood:	n/a	chr2:54308929-54308938 chr2:54309019-54309026
47	EGR1	chr2:54308779-54309009	K562	blood:	n/a	n/a
48	EP300	chr2:54308656-54309176	GM12878	blood:	n/a	n/a
49	ELF1	chr2:54308701-54309265	GM12878	blood:	n/a	n/a
50	ATF3	chr2:54308822-54309096	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:190092651..190093439-chr2:54308392..54308957,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272156	TF binding region
ENSG00000241114	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10183655	0.83[CHD][hapmap]
rs10496028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11676462	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11890838	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs11896815	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11898855	0.82[AFR][1000 genomes]
rs17039547	0.89[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17045452	0.85[CHD][hapmap];0.80[GIH][hapmap]
rs17045474	0.86[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045488	0.86[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1877908	0.88[CHD][hapmap]
rs2287643	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2357896	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2909459	1.00[YRI][hapmap]
rs34773403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3731967	0.85[CHD][hapmap];0.85[GIH][hapmap]
rs4671861	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55649409	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55705819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55930424	0.87[AFR][1000 genomes]
rs56193146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62137964	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62137976	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62137980	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62140990	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62141002	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545381	0.85[AFR][1000 genomes]
rs6545386	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6713088	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs6714450	0.85[AFR][1000 genomes]
rs6721970	0.91[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6751105	0.85[CHD][hapmap]
rs7559384	0.81[ASN][1000 genomes]
rs7565453	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7573551	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7576901	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7590819	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs805316	0.91[LWK][hapmap];0.91[YRI][hapmap]
rs805321	0.83[JPT][hapmap]
rs805328	0.88[JPT][hapmap]
rs805338	1.00[YRI][hapmap]
rs805351	0.84[JPT][hapmap]
rs805352	0.86[CHD][hapmap];0.93[GIH][hapmap]
rs805365	0.86[CHD][hapmap];0.93[GIH][hapmap]
rs805399	0.85[GIH][hapmap];0.89[JPT][hapmap]
rs805404	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs805408	0.89[JPT][hapmap]
rs805426	0.93[GIH][hapmap];0.83[JPT][hapmap]
rs805446	1.00[YRI][hapmap]
rs805449	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv3425103	chr2:54305541-54309163	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34498089	ACYP2	cis	multi-tissue	Pritchard
rs34498089	PSME4	cis	lymphoblastoid	seeQTL
rs34498089	MTIF2	cis	cerebellum	SCAN
rs34498089	PRDXDD1P	cis	parietal	SCAN
rs34498089	PSME4	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54280800-54310000	Weak transcription	Ovary	ovary
2	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
3	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
5	chr2:54287000-54310000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
7	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:54293600-54310600	Weak transcription	HSMM	muscle
9	chr2:54294800-54315000	Weak transcription	Fetal Intestine Small	intestine
10	chr2:54295200-54312200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:54295400-54309800	Weak transcription	Fetal Brain Male	brain
12	chr2:54302200-54310600	Weak transcription	A549	lung
13	chr2:54302600-54310400	Weak transcription	Osteobl	bone
14	chr2:54302800-54317800	Weak transcription	Left Ventricle	heart
15	chr2:54305000-54315000	Weak transcription	Fetal Intestine Large	intestine
16	chr2:54305000-54315200	Weak transcription	Pancreas	Pancrea
17	chr2:54305400-54321600	Weak transcription	Lung	lung
18	chr2:54306600-54315400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:54307400-54309800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:54307400-54310200	Weak transcription	Brain Anterior Caudate	brain
21	chr2:54307400-54310200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:54307400-54310200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:54307400-54319400	Weak transcription	Primary T cells from cord blood	blood
24	chr2:54307600-54309800	Weak transcription	Brain Substantia Nigra	brain
25	chr2:54308200-54309400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:54308200-54309400	Flanking Active TSS	GM12878-XiMat	blood
27	chr2:54308200-54309800	Enhancers	HMEC	breast
28	chr2:54308200-54310200	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:54308400-54309000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:54308400-54309000	Strong transcription	Fetal Muscle Leg	muscle
31	chr2:54308400-54309400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:54308400-54309400	Enhancers	NHEK	skin
33	chr2:54308400-54310000	Weak transcription	Brain Angular Gyrus	brain
34	chr2:54308600-54309000	Enhancers	Primary B cells from peripheral blood	blood
35	chr2:54308600-54309200	Enhancers	NH-A	brain
36	chr2:54308600-54309400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:54308800-54309000	Genic enhancers	K562	blood
38	chr2:54308800-54309200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:54308800-54309200	Enhancers	Esophagus	oesophagus

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