Variant report

Variant	rs2239699
Chromosome Location	chr3:52827915-52827916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52818572..52822409-chr3:52823256..52828567,5	K562	blood:
2	chr3:52802780..52807602-chr3:52827391..52831755,5	K562	blood:
3	chr3:52827101..52830669-chr3:52833208..52834941,3	K562	blood:
4	chr3:52827519..52829330-chr3:52834424..52837850,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162267	Chromatin interaction
ENSG00000114904	Chromatin interaction
ENSG00000055957	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1014969	0.84[JPT][hapmap]
rs1029871	0.84[JPT][hapmap]
rs1042779	0.90[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10510760	0.84[JPT][hapmap]
rs1075653	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1076425	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780035	0.84[JPT][hapmap]
rs10865973	0.84[JPT][hapmap]
rs10865974	0.84[JPT][hapmap]
rs11130310	0.89[JPT][hapmap]
rs11130312	0.84[JPT][hapmap]
rs11130315	0.84[JPT][hapmap]
rs11130317	0.84[JPT][hapmap]
rs11130323	0.84[JPT][hapmap]
rs11714419	0.84[JPT][hapmap]
rs11716747	0.84[JPT][hapmap]
rs11717836	0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12487591	0.84[JPT][hapmap]
rs12488461	0.89[JPT][hapmap]
rs12496634	0.84[JPT][hapmap]
rs12497998	0.84[JPT][hapmap]
rs12635140	0.84[JPT][hapmap]
rs13064064	0.84[JPT][hapmap]
rs13068293	0.84[JPT][hapmap]
rs13071584	0.84[JPT][hapmap]
rs13079063	0.89[JPT][hapmap]
rs13082208	0.87[JPT][hapmap]
rs13082960	0.83[JPT][hapmap]
rs13085895	0.84[JPT][hapmap]
rs1561337	0.84[JPT][hapmap]
rs1866268	0.84[JPT][hapmap]
rs2019065	0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2028216	0.84[JPT][hapmap]
rs2071506	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071507	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071508	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072390	0.84[JPT][hapmap]
rs2079929	0.84[JPT][hapmap]
rs2083180	0.84[JPT][hapmap]
rs2159644	0.84[JPT][hapmap]
rs2164884	0.88[JPT][hapmap]
rs2164885	0.89[JPT][hapmap]
rs2230535	0.84[JPT][hapmap]
rs2239549	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239550	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239551	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240919	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2240920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2268024	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2268025	0.84[JPT][hapmap]
rs2268026	0.84[JPT][hapmap]
rs2268027	0.83[JPT][hapmap]
rs2270197	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284350	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284351	0.90[ASN][1000 genomes]
rs2286798	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289247	0.84[JPT][hapmap]
rs2289250	0.84[JPT][hapmap]
rs2300149	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302417	0.80[ASN][1000 genomes]
rs2336149	0.84[JPT][hapmap]
rs2336545	0.84[JPT][hapmap]
rs2535629	0.80[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2710323	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2710331	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33967311	0.84[JPT][hapmap]
rs34017441	0.89[JPT][hapmap]
rs35526119	0.84[JPT][hapmap]
rs3733039	0.84[JPT][hapmap]
rs3733041	0.84[JPT][hapmap]
rs3733045	0.84[JPT][hapmap]
rs3755798	0.84[JPT][hapmap]
rs3755806	0.84[JPT][hapmap]
rs3774354	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774355	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774365	0.84[JPT][hapmap]
rs3774366	0.84[JPT][hapmap]
rs4687548	0.84[JPT][hapmap]
rs4687550	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4687551	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687552	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687638	0.84[JPT][hapmap]
rs4687650	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4687654	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445535	0.84[JPT][hapmap]
rs6617	0.84[JPT][hapmap]
rs6762813	0.84[JPT][hapmap]
rs6778329	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs678	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792369	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804145	0.84[JPT][hapmap]
rs6976	0.84[JPT][hapmap]
rs736408	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs746694	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7611731	0.84[JPT][hapmap]
rs7622694	0.84[JPT][hapmap]
rs7624716	0.84[JPT][hapmap]
rs767418	0.83[JPT][hapmap]
rs8906	0.84[JPT][hapmap]
rs9324	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881468	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998909	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2239699	PBRM1	cis	Thyroid	GTEx
rs2239699	NT5DC2	cis	multi-tissue	Pritchard
rs2239699	MUSTN1	cis	Artery Aorta	GTEx
rs2239699	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2239699	ITIH3	cis	multi-tissue	Pritchard
rs2239699	FLJ12442	cis	multi-tissue	Pritchard
rs2239699	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs2239699	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs2239699	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52824000-52832800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52825800-52836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:52826000-52829000	Enhancers	Fetal Muscle Leg	muscle
4	chr3:52826400-52828200	Enhancers	Liver	Liver
5	chr3:52826600-52828800	Weak transcription	Pancreas	Pancrea
6	chr3:52827000-52828000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:52827000-52828000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr3:52827000-52830600	Enhancers	Spleen	Spleen
9	chr3:52827400-52828400	Weak transcription	Right Ventricle	heart
10	chr3:52827400-52828400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
11	chr3:52827400-52829000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:52827400-52829000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:52827600-52828000	Enhancers	Stomach Mucosa	stomach
14	chr3:52827600-52828200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:52827600-52828200	Enhancers	HSMMtube	muscle
16	chr3:52827600-52829000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:52827600-52829800	Flanking Active TSS	HepG2	liver
18	chr3:52827800-52829200	Enhancers	Fetal Intestine Small	intestine
19	chr3:52827800-52829400	Enhancers	Fetal Intestine Large	intestine
20	chr3:52827800-52830000	Enhancers	Fetal Muscle Trunk	muscle
21	chr3:52827800-52832000	Weak transcription	HSMM	muscle

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