Variant report

Variant	rs2808673
Chromosome Location	chr9:100468218-100468219
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100462976..100466831-chr9:100467484..100471759,4	K562	blood:
2	chr9:100466290..100468242-chr9:100471348..100474178,4	K562	blood:
3	chr9:100466474..100468807-chr9:100682892..100684747,2	MCF-7	breast:
4	chr9:100465031..100468402-chr9:100745252..100748120,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10983030	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10983447	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12378130	0.83[ASN][1000 genomes]
rs12379552	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1800975	1.00[CEU][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2026132	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2036959	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668792	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668793	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2668798	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2773347	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2773351	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2805767	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2805775	0.87[EUR][1000 genomes]
rs2805777	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2805779	0.96[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2805824	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2805825	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2805826	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2805828	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2805829	0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2805832	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2805837	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2805839	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2805840	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2808668	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2808675	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808683	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2808685	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808686	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808687	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808689	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808691	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808692	0.92[EUR][1000 genomes]
rs2808694	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2808701	0.89[EUR][1000 genomes]
rs2808703	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6478325	0.86[EUR][1000 genomes]
rs7465737	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs958346	0.96[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2808673	XPA	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100462400-100472800	Weak transcription	Brain Substantia Nigra	brain
2	chr9:100465400-100469000	Enhancers	HMEC	breast
3	chr9:100465600-100468600	Enhancers	HUVEC	blood vessel
4	chr9:100465600-100468800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:100465600-100468800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr9:100466400-100468400	Enhancers	Osteobl	bone
7	chr9:100466600-100468600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:100466800-100468800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:100466800-100472800	Weak transcription	K562	blood
10	chr9:100467000-100468600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr9:100467000-100468600	Enhancers	NHEK	skin
12	chr9:100467000-100468800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:100467200-100468400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr9:100467200-100468400	Weak transcription	A549	lung
15	chr9:100467200-100472800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:100467200-100476400	Weak transcription	Fetal Intestine Large	intestine
17	chr9:100467600-100468400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:100467600-100468600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr9:100467600-100469000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr9:100467800-100468400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr9:100467800-100468400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr9:100467800-100468400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:100467800-100468600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:100468000-100468600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr9:100468000-100472600	Weak transcription	Hela-S3	cervix
26	chr9:100468000-100476600	Weak transcription	GM12878-XiMat	blood
27	chr9:100468200-100468400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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