Variant report

Variant	rs16869724
Chromosome Location	chr8:103688476-103688477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103686012..103689687-chr8:103690179..103693773,3	K562	blood:
2	chr8:103677991..103679955-chr8:103687094..103689017,2	K562	blood:
3	chr8:103687333..103690128-chr8:103818672..103821393,3	MCF-7	breast:
4	chr8:103687457..103689575-chr8:103691339..103694082,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253669	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10955288	0.88[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap]
rs12546601	0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12547574	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12547834	0.88[CEU][hapmap]
rs12548858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12549399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12674646	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12675196	0.90[EUR][1000 genomes]
rs12675239	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12680362	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12680598	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12680908	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12682093	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1318752	0.84[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap]
rs16869664	0.88[CEU][hapmap];0.81[JPT][hapmap];0.83[AFR][1000 genomes]
rs16869676	0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16869695	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2388192	0.83[AFR][1000 genomes]
rs2436946	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2471847	0.83[ASN][1000 genomes]
rs2511701	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2511718	0.83[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs2511719	0.82[ASN][1000 genomes]
rs2511730	0.83[ASN][1000 genomes]
rs2513924	1.00[ASW][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes]
rs2734824	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2916570	0.83[ASN][1000 genomes]
rs3018443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56398883	0.83[AFR][1000 genomes]
rs56929055	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60320584	0.83[AFR][1000 genomes]
rs72685103	0.83[AFR][1000 genomes]
rs72685104	0.83[AFR][1000 genomes]
rs72685109	0.83[AFR][1000 genomes]
rs72685110	0.92[EUR][1000 genomes]
rs72685117	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72685118	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72685123	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72685128	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73276720	0.84[EUR][1000 genomes]
rs9642980	0.85[TSI][hapmap]
rs980112	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1026755	chr8:103676970-103728556	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1018625	chr8:103676970-103729197	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16869724	SPAG1	cis	parietal	SCAN
rs16869724	ODF1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103675400-103698200	Weak transcription	Osteobl	bone
2	chr8:103675600-103692800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr8:103679400-103689400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr8:103679800-103706400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:103688000-103688800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr8:103688000-103688800	Enhancers	Lung	lung
7	chr8:103688200-103688800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr8:103688200-103688800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr8:103688200-103688800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr8:103688200-103689000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr8:103688400-103688800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr8:103688400-103689000	Enhancers	K562	blood
13	chr8:103688400-103690200	ZNF genes & repeats	Fetal Intestine Small	intestine

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