Variant report

Variant	rs6656538
Chromosome Location	chr1:86456685-86456686
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	chr1:86452263..86454852-chr1:86455069..86456770,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10873740	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs11161714	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11161715	0.87[CHB][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11161716	0.86[CHB][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11161717	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs11161719	0.87[EUR][1000 genomes]
rs12023979	0.87[ASN][1000 genomes]
rs12025292	0.86[CHB][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12025755	0.91[CHB][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12029153	0.87[ASN][1000 genomes]
rs12031047	0.87[ASN][1000 genomes]
rs12031105	0.87[ASN][1000 genomes]
rs12031129	0.87[ASN][1000 genomes]
rs12039529	0.86[CHB][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12040977	0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs12040981	0.91[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12127813	0.91[CHB][hapmap];0.85[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12135956	0.87[ASN][1000 genomes]
rs12403155	0.87[ASN][1000 genomes]
rs12404609	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs12407101	0.87[ASN][1000 genomes]
rs1324899	0.88[EUR][1000 genomes]
rs17405077	0.84[CHB][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap]
rs17405131	0.85[ASN][1000 genomes]
rs2390005	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2390006	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2390007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2390008	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28480217	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4272648	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4306156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4350224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4912453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4912454	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55892290	0.86[ASN][1000 genomes]
rs55904471	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs55958413	0.86[ASN][1000 genomes]
rs56278817	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61617423	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6576795	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6672098	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66724882	0.87[ASN][1000 genomes]
rs6704536	0.87[CHB][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7411585	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7415711	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7514604	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516083	0.87[ASN][1000 genomes]
rs7547149	0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7551636	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv462395	chr1:86379514-86457334	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv546726	chr1:86379514-86457334	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv546758	chr1:86438327-86483632	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3340591	chr1:86439980-86459810	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1012808	chr1:86455710-86470489	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6656538	COL24A1	cis	Artery Tibial	GTEx
rs6656538	COL24A1	cis	multi-tissue	Pritchard
rs6656538	COL24A1	cis	Nerve Tibial	GTEx
rs6656538	COL24A1	cis	Artery Aorta	GTEx
rs6656538	COL24A1	cis	Thyroid	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86449400-86466200	Weak transcription	Fetal Lung	lung
2	chr1:86454400-86458200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:86455600-86457000	Flanking Active TSS	GM12878-XiMat	blood
4	chr1:86456000-86457000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr1:86456200-86457200	Enhancers	Dnd41	blood
6	chr1:86456200-86457600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:86456200-86464600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:86456400-86457400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:86456600-86457200	Flanking Active TSS	Primary hematopoietic stem cells	blood

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