Variant report

Variant	rs6424444
Chromosome Location	chr1:72191607-72191608
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	chr1:72187008..72189556-chr1:72189903..72192438,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10789323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs10789324	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11209831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12124058	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12125609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12135360	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1213556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1213558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407479	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs12410430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1350644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1459791	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1459792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1459794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459800	0.81[YRI][hapmap]
rs1762722	0.81[AMR][1000 genomes]
rs1762727	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2422030	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2422031	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2794304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2794305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4649942	0.81[EUR][1000 genomes]
rs497074	0.86[JPT][hapmap]
rs515890	0.94[EUR][1000 genomes]
rs531071	0.81[CHB][hapmap]
rs538127	0.86[JPT][hapmap]
rs551411	0.93[EUR][1000 genomes]
rs6657641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6686704	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6695498	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949599	chr1:71655652-72327802	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1007250	chr1:71998391-72350683	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv534992	chr1:71998391-72350683	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1003446	chr1:72060680-72419918	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv461884	chr1:72077549-72238691	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv546476	chr1:72077549-72238691	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv461895	chr1:72079898-72206799	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv546477	chr1:72079898-72206799	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1006188	chr1:72081620-72215373	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv534993	chr1:72081620-72215373	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1008210	chr1:72099161-72374197	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv533779	chr1:72124095-72241965	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv830181	chr1:72155983-72296578	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72189400-72197000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:72189600-72197600	Weak transcription	Thymus	Thymus
3	chr1:72191400-72198800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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