Variant report

Variant	rs58240943
Chromosome Location	chr12:39818059-39818060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39815775..39818623-chr12:39834712..39837857,3	MCF-7	breast:
2	chr12:39815681..39818065-chr12:39831801..39835369,3	K562	blood:
3	chr12:39814931..39819046-chr12:39820377..39824549,5	K562	blood:

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10876886	0.83[ASN][1000 genomes]
rs10876972	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876989	0.80[EUR][1000 genomes]
rs10877100	0.82[EUR][1000 genomes]
rs11171923	0.84[ASN][1000 genomes]
rs11172081	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172108	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172120	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172174	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172183	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172235	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172264	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11172293	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172357	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11172386	0.84[EUR][1000 genomes]
rs11172392	0.84[EUR][1000 genomes]
rs11172492	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11172493	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11172526	0.83[EUR][1000 genomes]
rs11172592	0.83[EUR][1000 genomes]
rs11830643	0.83[ASN][1000 genomes]
rs12228767	0.83[ASN][1000 genomes]
rs12424345	0.84[ASN][1000 genomes]
rs1512936	0.83[ASN][1000 genomes]
rs1567739	0.84[ASN][1000 genomes]
rs2388320	0.84[ASN][1000 genomes]
rs4320988	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4390378	0.85[EUR][1000 genomes]
rs4492858	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4500523	0.84[EUR][1000 genomes]
rs4564382	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58613501	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59695906	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60900225	0.80[EUR][1000 genomes]
rs6581187	0.83[EUR][1000 genomes]
rs73094410	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962283	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964447	0.83[ASN][1000 genomes]
rs7965222	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968837	0.82[EUR][1000 genomes]
rs7974928	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39785000-39829200	Weak transcription	K562	blood
2	chr12:39794200-39824800	Weak transcription	Right Atrium	heart
3	chr12:39806600-39834200	Weak transcription	Hela-S3	cervix
4	chr12:39808600-39821600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:39808600-39830800	Weak transcription	Fetal Brain Female	brain
6	chr12:39810000-39821000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:39812600-39820200	Weak transcription	HepG2	liver
8	chr12:39812800-39820200	Weak transcription	HMEC	breast
9	chr12:39813600-39833400	Weak transcription	Brain Germinal Matrix	brain
10	chr12:39813800-39820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:39814200-39821200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:39814200-39821400	Weak transcription	Placenta	Placenta
13	chr12:39814200-39825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:39814400-39833800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:39814800-39820800	Weak transcription	A549	lung
16	chr12:39815000-39818200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:39816000-39818400	Enhancers	Fetal Heart	heart
18	chr12:39816000-39834000	Weak transcription	Left Ventricle	heart
19	chr12:39816800-39819200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:39817400-39824600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:39817400-39824600	Weak transcription	Right Ventricle	heart

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