Variant report

Variant	rs12200084
Chromosome Location	chr6:30040603-30040604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30039276..30042217-chr6:30067253..30069841,2	K562	blood:
2	chr6:30039304..30041261-chr6:30060958..30063803,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10947050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752303	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12193100	0.84[EUR][1000 genomes]
rs12193110	0.81[EUR][1000 genomes]
rs12195207	0.85[EUR][1000 genomes]
rs12195260	0.86[EUR][1000 genomes]
rs12202241	0.86[EUR][1000 genomes]
rs12206499	0.85[EUR][1000 genomes]
rs2071568	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2275855	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2394247	0.80[EUR][1000 genomes]
rs2508035	0.84[EUR][1000 genomes]
rs2523935	0.81[EUR][1000 genomes]
rs33959627	0.93[AFR][1000 genomes]
rs35066870	0.87[EUR][1000 genomes]
rs35159526	0.87[EUR][1000 genomes]
rs3807031	0.93[AFR][1000 genomes]
rs3823352	0.86[EUR][1000 genomes]
rs3823353	0.85[EUR][1000 genomes]
rs3823354	0.86[EUR][1000 genomes]
rs3823355	0.86[EUR][1000 genomes]
rs3823358	0.87[EUR][1000 genomes]
rs3823369	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3910312	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4248141	0.80[EUR][1000 genomes]
rs4248142	0.80[EUR][1000 genomes]
rs4248143	0.80[EUR][1000 genomes]
rs4711206	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711207	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713269	0.80[EUR][1000 genomes]
rs4713270	0.80[EUR][1000 genomes]
rs4713274	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4713275	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4713279	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713281	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4947244	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4959010	0.88[EUR][1000 genomes]
rs4959038	0.80[EUR][1000 genomes]
rs4959039	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4959040	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457127	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6903753	0.88[EUR][1000 genomes]
rs6904029	0.88[EUR][1000 genomes]
rs6916422	0.85[EUR][1000 genomes]
rs6916451	0.85[EUR][1000 genomes]
rs6935024	0.80[EUR][1000 genomes]
rs7766469	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295825	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9295826	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295829	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295830	0.96[AFR][1000 genomes]
rs9348835	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357088	0.84[EUR][1000 genomes]
rs9357092	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366750	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9366752	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378141	0.80[EUR][1000 genomes]
rs9378142	0.84[EUR][1000 genomes]
rs9380150	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393984	0.83[EUR][1000 genomes]
rs9393986	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393987	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393988	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393989	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405044	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv884049	chr6:30037353-30047403	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12200084	LOC730399///LOC731974	Cis_1M	lymphoblastoid	RTeQTL
rs12200084	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL
rs12200084	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs12200084	HLA.A29.1	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30035600-30041000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:30036600-30040800	Strong transcription	NHEK	skin
3	chr6:30036800-30042400	Weak transcription	Hela-S3	cervix
4	chr6:30038000-30041200	Weak transcription	Pancreas	Pancrea
5	chr6:30038000-30041200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:30038000-30041400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:30038000-30041800	Weak transcription	Ovary	ovary
8	chr6:30038400-30044000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:30038600-30042000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:30038800-30041200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:30038800-30043400	Weak transcription	Dnd41	blood
12	chr6:30039000-30042000	Weak transcription	Lung	lung
13	chr6:30039600-30041000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:30039600-30042200	Weak transcription	Right Atrium	heart
15	chr6:30039800-30041200	Weak transcription	Esophagus	oesophagus
16	chr6:30039800-30041800	Weak transcription	Gastric	stomach
17	chr6:30040600-30040800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:30040600-30041000	Enhancers	HepG2	liver
19	chr6:30040600-30041200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:30040600-30041800	Weak transcription	HMEC	breast

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