Variant report

Variant	rs58238388
Chromosome Location	chr1:174735009-174735010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174733969..174735629-chr1:174967273..174968966,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10912808	1.00[EUR][1000 genomes]
rs10912809	1.00[EUR][1000 genomes]
rs10912815	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912816	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912818	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912819	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912847	1.00[EUR][1000 genomes]
rs10912851	1.00[EUR][1000 genomes]
rs10912858	1.00[EUR][1000 genomes]
rs10912864	1.00[EUR][1000 genomes]
rs11806870	1.00[EUR][1000 genomes]
rs12057161	1.00[EUR][1000 genomes]
rs12057359	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12064144	1.00[EUR][1000 genomes]
rs12066268	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066421	1.00[EUR][1000 genomes]
rs12067791	1.00[EUR][1000 genomes]
rs12068625	1.00[EUR][1000 genomes]
rs12069689	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12070082	1.00[EUR][1000 genomes]
rs12072909	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075193	1.00[EUR][1000 genomes]
rs12077283	1.00[EUR][1000 genomes]
rs12077880	1.00[EUR][1000 genomes]
rs12078714	1.00[EUR][1000 genomes]
rs12080070	1.00[EUR][1000 genomes]
rs12080242	1.00[EUR][1000 genomes]
rs12084999	1.00[EUR][1000 genomes]
rs12088650	1.00[EUR][1000 genomes]
rs12096717	1.00[EUR][1000 genomes]
rs1231828	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12354111	1.00[EUR][1000 genomes]
rs1329280	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1612104	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1618234	1.00[EUR][1000 genomes]
rs1653631	1.00[EUR][1000 genomes]
rs1653633	1.00[EUR][1000 genomes]
rs1653637	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847457	1.00[EUR][1000 genomes]
rs173000	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1754356	1.00[EUR][1000 genomes]
rs17838246	1.00[EUR][1000 genomes]
rs189141	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2116515	1.00[EUR][1000 genomes]
rs2760059	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2981891	1.00[EUR][1000 genomes]
rs2981895	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2987871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2987878	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3018408	0.95[AMR][1000 genomes]
rs3123641	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332766	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332775	1.00[EUR][1000 genomes]
rs332780	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332785	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332790	1.00[EUR][1000 genomes]
rs332792	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs333419	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs333425	1.00[EUR][1000 genomes]
rs333434	1.00[EUR][1000 genomes]
rs35582650	1.00[EUR][1000 genomes]
rs392368	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4290116	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4309037	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs454643	0.89[AMR][1000 genomes]
rs55659406	1.00[EUR][1000 genomes]
rs56106555	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56357087	1.00[EUR][1000 genomes]
rs59073370	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60283543	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6672781	1.00[EUR][1000 genomes]
rs6696432	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6701696	1.00[EUR][1000 genomes]
rs74126848	1.00[EUR][1000 genomes]
rs74126851	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126855	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74128516	1.00[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	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv548197	chr1:174731596-174741017	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv548198	chr1:174731596-174800872	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174711800-174745600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174720200-174739000	Weak transcription	GM12878-XiMat	blood
3	chr1:174723200-174739000	Weak transcription	Primary T cells from cord blood	blood
4	chr1:174730400-174735800	Weak transcription	Gastric	stomach
5	chr1:174733800-174735200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:174734200-174737400	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:174735000-174736400	Enhancers	Fetal Intestine Small	intestine
8	chr1:174735000-174736600	Enhancers	Fetal Intestine Large	intestine

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