Variant report

Variant	rs6452904
Chromosome Location	chr5:89997358-89997359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89996062..89998352-chr5:90001342..90003176,2	K562	blood:
2	chr5:89994085..89995994-chr5:89996980..89998521,2	K562	blood:
3	chr5:89996062..89999170-chr5:90000730..90003176,4	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10036258	0.87[EUR][1000 genomes]
rs10036980	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10043836	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10045236	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10045394	0.83[EUR][1000 genomes]
rs10058765	0.80[ASN][1000 genomes]
rs10060365	0.83[ASN][1000 genomes]
rs10060427	0.80[ASN][1000 genomes]
rs10062714	0.80[ASN][1000 genomes]
rs10062924	0.80[ASN][1000 genomes]
rs10067181	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10068473	0.87[ASN][1000 genomes]
rs1014750	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1028191	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1028192	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1033290	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10514333	0.88[ASN][1000 genomes]
rs10942605	0.89[ASN][1000 genomes]
rs10942606	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1160121	0.89[ASN][1000 genomes]
rs12188928	0.88[ASN][1000 genomes]
rs12516985	0.80[ASN][1000 genomes]
rs12652606	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12657264	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13167491	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673379	0.80[ASN][1000 genomes]
rs16868957	0.80[ASN][1000 genomes]
rs1878878	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1993474	0.91[ASN][1000 genomes]
rs2176624	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222242	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2366777	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28517617	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28550273	0.80[ASN][1000 genomes]
rs28587199	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3927265	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4379236	0.80[ASN][1000 genomes]
rs4916681	0.80[ASN][1000 genomes]
rs4916682	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4916684	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4916686	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916813	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4916814	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6452905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452906	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6861525	0.87[ASN][1000 genomes]
rs6863710	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6881412	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6898209	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7703530	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7703588	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7714506	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7723259	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7724806	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7726624	0.81[ASN][1000 genomes]
rs7729703	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7732169	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9293550	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs963866	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs977906	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv1032225	chr5:89940489-89999954	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv934323	chr5:89968158-90111853	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv882368	chr5:89990324-90012379	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv522663	chr5:89995803-89998454	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89950400-90033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:89979200-90002600	Weak transcription	Brain Anterior Caudate	brain
3	chr5:89982000-90004600	Weak transcription	Fetal Brain Female	brain
4	chr5:89987000-90001200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:89987800-90007200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:89990600-90001200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:89991200-90001000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:89991800-90014000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:89992400-89999800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:89993600-90001200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:89994600-89997800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:89994600-90001600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:89994800-89999200	Weak transcription	K562	blood
14	chr5:89995000-90001600	Weak transcription	Brain Germinal Matrix	brain
15	chr5:89995000-90025800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:89995400-89997800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:89995600-89998800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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