Variant report

Variant	rs6792369
Chromosome Location	chr3:52811172-52811173
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52810201..52813170-chr3:52814062..52816264,2	K562	blood:

Variant related genes	Relation type
ENSG00000055957	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1014969	0.84[AMR][1000 genomes]
rs1029871	0.82[EUR][1000 genomes]
rs1042779	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1075653	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1076425	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130317	0.80[AMR][1000 genomes]
rs11130323	0.80[AMR][1000 genomes]
rs11130325	0.80[AMR][1000 genomes]
rs11130327	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11717836	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12496634	0.80[AMR][1000 genomes]
rs12497998	0.80[EUR][1000 genomes]
rs13061423	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13071584	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13082960	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13095332	0.81[EUR][1000 genomes]
rs2019065	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071506	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2071507	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2071508	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2098167	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2230534	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2230535	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2239549	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239550	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239551	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239699	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240919	0.87[ASN][1000 genomes]
rs2240920	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2268023	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2268024	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2268025	0.82[EUR][1000 genomes]
rs2268026	0.80[AMR][1000 genomes]
rs2270197	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2284350	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2284351	0.83[ASN][1000 genomes]
rs2286798	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300149	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302417	0.89[ASN][1000 genomes]
rs2336542	0.80[AMR][1000 genomes]
rs2336545	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2535629	0.89[ASN][1000 genomes]
rs2710323	0.88[ASN][1000 genomes]
rs34291015	0.80[AMR][1000 genomes]
rs3755799	0.81[AMR][1000 genomes]
rs3774354	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774355	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687551	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4687650	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4687654	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255396	0.80[AMR][1000 genomes]
rs67539070	0.80[AMR][1000 genomes]
rs6778329	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs678	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs736408	0.86[ASN][1000 genomes]
rs746694	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9324	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9881468	0.86[ASN][1000 genomes]
rs998909	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6792369	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs6792369	ITIH4-AS1	cis	Artery Aorta	GTEx
rs6792369	MUSTN1	cis	Artery Aorta	GTEx
rs6792369	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs6792369	PBRM1	cis	Thyroid	GTEx
rs6792369	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52805600-52825800	Weak transcription	Right Ventricle	heart
2	chr3:52805800-52812000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:52806000-52811600	Weak transcription	Adipose Nuclei	Adipose
4	chr3:52808600-52811200	Enhancers	Fetal Intestine Large	intestine
5	chr3:52808600-52812000	Enhancers	Fetal Intestine Small	intestine
6	chr3:52809000-52811400	Enhancers	Stomach Mucosa	stomach
7	chr3:52810000-52811600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:52810200-52811600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:52810200-52812200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:52810200-52812400	Weak transcription	Fetal Heart	heart
11	chr3:52810200-52816600	Enhancers	HepG2	liver
12	chr3:52810400-52811600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:52810600-52812000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:52810800-52812000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:52810800-52815600	Weak transcription	Fetal Thymus	thymus
16	chr3:52811000-52812600	Active TSS	Liver	Liver
17	chr3:52811000-52812600	Enhancers	Pancreas	Pancrea

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