Variant report

Variant	rs9701002
Chromosome Location	chr1:86469506-86469507
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12079919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1698735	0.89[YRI][hapmap]
rs1698742	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs1698743	0.87[ASW][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1698744	0.89[YRI][hapmap]
rs2390052	0.89[YRI][hapmap]
rs471070	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs473232	0.89[YRI][hapmap]
rs474106	0.89[YRI][hapmap]
rs477562	0.87[AFR][1000 genomes]
rs477862	0.89[YRI][hapmap]
rs485816	0.82[YRI][hapmap]
rs489267	0.85[AFR][1000 genomes]
rs494796	0.93[YRI][hapmap]
rs500756	0.89[AFR][1000 genomes]
rs511363	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs511732	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs514185	0.89[YRI][hapmap]
rs516799	0.87[AFR][1000 genomes]
rs518538	0.87[AFR][1000 genomes]
rs519361	0.85[AFR][1000 genomes]
rs521253	0.87[AFR][1000 genomes]
rs532684	0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs538256	0.87[ASW][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs541936	0.80[YRI][hapmap]
rs547023	0.87[AFR][1000 genomes]
rs551670	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs567565	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs567617	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs569409	0.87[ASW][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs570172	0.86[AFR][1000 genomes]
rs574780	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs580540	0.87[AFR][1000 genomes]
rs582517	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs586240	0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs586629	0.85[AFR][1000 genomes]
rs589343	0.89[YRI][hapmap]
rs599761	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs612256	0.87[ASW][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs615805	0.89[AFR][1000 genomes]
rs616281	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs617652	0.81[AFR][1000 genomes]
rs631512	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs632295	0.87[AFR][1000 genomes]
rs632697	0.87[AFR][1000 genomes]
rs634946	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs635391	0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs635397	0.85[AFR][1000 genomes]
rs635713	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs636210	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs641712	0.89[YRI][hapmap]
rs647380	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs648866	0.87[AFR][1000 genomes]
rs650216	0.87[AFR][1000 genomes]
rs658313	0.80[YRI][hapmap]
rs663463	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs663901	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs664099	0.85[AFR][1000 genomes]
rs664412	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs679256	0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs680179	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9701002	COL24A1	cis	parietal	SCAN
rs9701002	COL24A1	cis	Artery Tibial	GTEx
rs9701002	BCL10	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86459200-86472000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:86459200-86472200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:86464000-86469800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:86468400-86470400	Strong transcription	Fetal Lung	lung
5	chr1:86469000-86469800	Strong transcription	Fetal Muscle Leg	muscle

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