Variant report

Variant	rs2282751
Chromosome Location	chr3:50291785-50291786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50291660-50292074	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:50291688-50291860	H1-hESC	embryonic stem cell:	n/a	n/a
3	NFYB	chr3:50291627-50291827	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:50291051-50292191	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50284602..50287815-chr3:50290818..50293169,4	K562	blood:
2	chr3:50283737..50287668-chr3:50290117..50294367,4	K562	blood:
3	chr3:50290143..50293966-chr3:50294360..50298503,5	K562	blood:
4	chr3:50291177..50293033-chr3:50365487..50367223,2	K562	blood:
5	chr3:50291693..50293673-chr3:50302164..50305046,2	K562	blood:
6	chr3:50263347..50265205-chr3:50290120..50292082,2	MCF-7	breast:
7	chr3:50272477..50276068-chr3:50288828..50297512,10	MCF-7	breast:

No data

Variant related genes	Relation type
GNAI2	TF binding region
ENSG00000114353	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000114383	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000230454	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1107265	0.82[MEX][hapmap]
rs11130248	0.84[CHD][hapmap]
rs12054403	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs12485390	0.83[JPT][hapmap]
rs12485909	0.81[CHD][hapmap]
rs12488302	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs12492880	0.84[CHD][hapmap]
rs12494414	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs12629572	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs1858828	0.84[LWK][hapmap];0.85[MKK][hapmap];0.83[AFR][1000 genomes]
rs1989839	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs2071203	0.84[CHD][hapmap]
rs2071204	0.84[CHD][hapmap]
rs2073499	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2073500	0.84[CHD][hapmap]
rs2233474	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2233476	0.84[CHD][hapmap]
rs2236944	0.84[CHD][hapmap]
rs2236946	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2236948	0.80[AMR][1000 genomes]
rs2236950	0.84[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2236951	0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs2236964	0.82[MEX][hapmap]
rs2282749	0.94[LWK][hapmap];0.82[AFR][1000 genomes]
rs2282753	0.82[MEX][hapmap]
rs2282754	0.82[MEX][hapmap]
rs2285043	0.84[CHD][hapmap]
rs2298953	0.81[CHD][hapmap]
rs2298954	0.81[CHD][hapmap]
rs3213621	0.84[CHD][hapmap]
rs35455589	0.82[CHD][hapmap]
rs35587949	0.84[CHD][hapmap]
rs3774753	0.81[CHD][hapmap]
rs3774755	0.82[CHD][hapmap]
rs4141060	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688682	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs4688732	0.84[CHD][hapmap]
rs4688734	0.84[CHD][hapmap]
rs4688741	0.81[CHD][hapmap]
rs57838764	0.83[ASN][1000 genomes]
rs6776145	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs734767	0.82[MEX][hapmap]
rs739431	0.96[GIH][hapmap]
rs743757	0.82[MEX][hapmap]
rs762705	0.86[ASN][1000 genomes]
rs7645537	0.81[CHD][hapmap]
rs9852677	0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs9883222	0.81[CHD][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
7	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
11	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
12	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
19	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
20	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
21	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
22	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
23	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
24	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
25	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
26	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
27	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
28	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2282751	PCBP4	cis	parietal	SCAN
rs2282751	RASSF1	cis	brain	BrainEAC
rs2282751	C3orf45	cis	cerebellum	SCAN
rs2282751	SLC25A20	cis	cerebellum	SCAN
rs2282751	DALRD3	cis	parietal	SCAN
rs2282751	TRAIP	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50276400-50294400	Genic enhancers	Lung	lung
2	chr3:50283400-50293200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:50283800-50294000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:50284200-50297000	Genic enhancers	Fetal Muscle Trunk	muscle
5	chr3:50284400-50292000	Weak transcription	Fetal Brain Male	brain
6	chr3:50284400-50293000	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr3:50284400-50295000	Genic enhancers	Spleen	Spleen
8	chr3:50284400-50295800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:50284400-50297000	Genic enhancers	Fetal Muscle Leg	muscle
10	chr3:50284600-50294000	Genic enhancers	Placenta	Placenta
11	chr3:50284800-50293000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:50284800-50294000	Weak transcription	Fetal Kidney	kidney
13	chr3:50284800-50300600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:50285200-50294400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:50285200-50296000	Strong transcription	Dnd41	blood
16	chr3:50285200-50296600	Strong transcription	Thymus	Thymus
17	chr3:50286000-50293000	Genic enhancers	HSMM	muscle
18	chr3:50286000-50293400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:50286000-50296200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:50286200-50293200	Genic enhancers	Brain Hippocampus Middle	brain
21	chr3:50286200-50293400	Strong transcription	GM12878-XiMat	blood
22	chr3:50286800-50293600	Strong transcription	Fetal Intestine Small	intestine
23	chr3:50286800-50297000	Weak transcription	A549	lung
24	chr3:50287200-50296400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:50287400-50293200	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr3:50287400-50294400	Genic enhancers	Adipose Nuclei	Adipose
27	chr3:50287600-50294000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:50287600-50295400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:50287800-50292200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:50287800-50297200	Weak transcription	Small Intestine	intestine
31	chr3:50288200-50292000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:50288200-50292000	Weak transcription	Psoas Muscle	Psoas
33	chr3:50288200-50293000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:50288200-50294800	Strong transcription	Fetal Intestine Large	intestine
35	chr3:50288200-50295600	Strong transcription	Fetal Thymus	thymus
36	chr3:50288600-50292400	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr3:50288600-50293200	Genic enhancers	Primary monocytes fromperipheralblood	blood
38	chr3:50288600-50294000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:50288600-50294000	Genic enhancers	HMEC	breast
40	chr3:50288600-50296200	Strong transcription	Primary T cells from cord blood	blood
41	chr3:50288600-50296600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:50288800-50291800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:50288800-50293200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:50288800-50295800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:50288800-50296000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:50289000-50292000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:50289000-50293000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:50289000-50293200	Genic enhancers	Monocytes-CD14+_RO01746	blood
49	chr3:50289000-50294000	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr3:50289000-50296000	Strong transcription	Rectal Smooth Muscle	rectum

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