Variant report

Variant	rs1498198
Chromosome Location	chr15:76350516-76350517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:76349182-76352137	A549	lung:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349476-76349484 chr15:76349960-76349981 chr15:76349958-76349976
2	CTCF	chr15:76349518-76350887	SK-N-SH	brain:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76195094..76197177-chr15:76350015..76352498,2	K562	blood:
2	chr15:76341281..76343239-chr15:76349906..76351616,2	MCF-7	breast:

Variant related genes	Relation type
C15orf27	TF binding region
NRG4	TF binding region
ENSG00000167196	Chromatin interaction

Extended variants
information (count: 178 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:174)

rs_ID	r²[population]
rs1039547	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13379955	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs1394122	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1498196	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1498197	1.00[EUR][1000 genomes]
rs1503955	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1532783	1.00[EUR][1000 genomes]
rs1562403	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1695365	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16967747	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs170830	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1874955	1.00[EUR][1000 genomes]
rs1874956	1.00[EUR][1000 genomes]
rs1910510	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1976328	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2133099	1.00[EUR][1000 genomes]
rs2133408	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2133409	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2133410	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2405578	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2441928	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2454209	1.00[CEU][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454210	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2454212	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2454470	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2454472	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2455897	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2460795	1.00[EUR][1000 genomes]
rs2460796	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2460801	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2469038	1.00[EUR][1000 genomes]
rs2469040	1.00[EUR][1000 genomes]
rs2593275	1.00[EUR][1000 genomes]
rs2593281	1.00[EUR][1000 genomes]
rs2593302	1.00[EUR][1000 genomes]
rs2604405	1.00[EUR][1000 genomes]
rs2648435	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2648437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2655126	1.00[EUR][1000 genomes]
rs2655137	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2947239	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2955772	0.81[LWK][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes]
rs2959851	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs334923	1.00[EUR][1000 genomes]
rs334937	1.00[EUR][1000 genomes]
rs334939	1.00[EUR][1000 genomes]
rs334940	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs334941	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs334947	0.84[YRI][hapmap]
rs334951	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs335673	1.00[EUR][1000 genomes]
rs335674	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs335676	0.85[EUR][1000 genomes]
rs335678	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs335683	1.00[EUR][1000 genomes]
rs335684	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs335687	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335693	0.85[EUR][1000 genomes]
rs335694	1.00[EUR][1000 genomes]
rs335695	1.00[EUR][1000 genomes]
rs335700	1.00[EUR][1000 genomes]
rs335701	1.00[EUR][1000 genomes]
rs335710	0.85[EUR][1000 genomes]
rs335713	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335717	1.00[EUR][1000 genomes]
rs335724	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335725	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335726	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335728	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335729	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs335730	1.00[EUR][1000 genomes]
rs335731	1.00[EUR][1000 genomes]
rs335732	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335733	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4482249	1.00[EUR][1000 genomes]
rs4489969	1.00[EUR][1000 genomes]
rs4886750	0.85[EUR][1000 genomes]
rs55665712	1.00[EUR][1000 genomes]
rs55719276	1.00[EUR][1000 genomes]
rs55782145	1.00[EUR][1000 genomes]
rs55828994	1.00[EUR][1000 genomes]
rs56139080	1.00[EUR][1000 genomes]
rs56167836	1.00[EUR][1000 genomes]
rs56173902	1.00[EUR][1000 genomes]
rs56218266	1.00[EUR][1000 genomes]
rs57011816	1.00[EUR][1000 genomes]
rs57127155	1.00[EUR][1000 genomes]
rs57141410	1.00[EUR][1000 genomes]
rs57429900	1.00[EUR][1000 genomes]
rs57737646	1.00[EUR][1000 genomes]
rs57968453	1.00[EUR][1000 genomes]
rs57971067	1.00[EUR][1000 genomes]
rs57973358	1.00[EUR][1000 genomes]
rs58044283	1.00[EUR][1000 genomes]
rs58170668	0.92[EUR][1000 genomes]
rs58399164	1.00[EUR][1000 genomes]
rs58717562	1.00[EUR][1000 genomes]
rs58789594	1.00[EUR][1000 genomes]
rs59143042	1.00[EUR][1000 genomes]
rs59690620	1.00[EUR][1000 genomes]
rs59819402	1.00[EUR][1000 genomes]
rs59839117	1.00[EUR][1000 genomes]
rs60088262	1.00[EUR][1000 genomes]
rs60155009	1.00[EUR][1000 genomes]
rs60191258	1.00[EUR][1000 genomes]
rs60817295	1.00[EUR][1000 genomes]
rs60846313	1.00[EUR][1000 genomes]
rs61240117	1.00[EUR][1000 genomes]
rs61521312	1.00[EUR][1000 genomes]
rs62027568	1.00[EUR][1000 genomes]
rs7168988	1.00[EUR][1000 genomes]
rs7173697	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7174280	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7174365	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7175758	1.00[EUR][1000 genomes]
rs7177048	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7180064	1.00[EUR][1000 genomes]
rs7181550	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7182720	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs74024005	1.00[EUR][1000 genomes]
rs74024006	1.00[EUR][1000 genomes]
rs74024007	1.00[EUR][1000 genomes]
rs74024009	1.00[EUR][1000 genomes]
rs74024011	1.00[EUR][1000 genomes]
rs74024014	1.00[EUR][1000 genomes]
rs74024015	1.00[EUR][1000 genomes]
rs74024016	1.00[EUR][1000 genomes]
rs74024017	1.00[EUR][1000 genomes]
rs74024020	1.00[EUR][1000 genomes]
rs74024021	0.83[EUR][1000 genomes]
rs74024022	1.00[EUR][1000 genomes]
rs74024023	1.00[EUR][1000 genomes]
rs74024028	1.00[EUR][1000 genomes]
rs74024029	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74024030	1.00[EUR][1000 genomes]
rs74024032	1.00[EUR][1000 genomes]
rs74024035	1.00[EUR][1000 genomes]
rs74024038	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74024039	1.00[EUR][1000 genomes]
rs74024040	1.00[EUR][1000 genomes]
rs74024041	1.00[EUR][1000 genomes]
rs74024042	1.00[EUR][1000 genomes]
rs74024043	1.00[EUR][1000 genomes]
rs74024044	1.00[EUR][1000 genomes]
rs74024045	1.00[EUR][1000 genomes]
rs74024047	1.00[EUR][1000 genomes]
rs74024048	1.00[EUR][1000 genomes]
rs74024049	1.00[EUR][1000 genomes]
rs74024051	1.00[EUR][1000 genomes]
rs74024052	1.00[EUR][1000 genomes]
rs74024053	1.00[EUR][1000 genomes]
rs74024059	1.00[EUR][1000 genomes]
rs74024060	1.00[EUR][1000 genomes]
rs74024063	1.00[EUR][1000 genomes]
rs74024064	1.00[EUR][1000 genomes]
rs74024065	1.00[EUR][1000 genomes]
rs74024071	1.00[EUR][1000 genomes]
rs74024073	1.00[EUR][1000 genomes]
rs8025372	1.00[EUR][1000 genomes]
rs8028084	1.00[EUR][1000 genomes]
rs8028766	1.00[EUR][1000 genomes]
rs8030102	1.00[CEU][hapmap]
rs8030469	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8030948	0.85[EUR][1000 genomes]
rs8031263	1.00[EUR][1000 genomes]
rs8033005	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8034430	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8035611	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8036952	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs8038729	0.92[EUR][1000 genomes]
rs9672219	1.00[EUR][1000 genomes]
rs974718	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904398	chr15:76220285-76359055	Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1617	chr15:76332103-76359435	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1048760	chr15:76334544-76496977	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1498198	FBXO22	cis	lymphoblastoid	seeQTL
rs1498198	FBXO22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76349400-76351000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:76349600-76350800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:76349600-76351400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:76349800-76351000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:76349800-76351200	Active TSS	Brain Angular Gyrus	brain
6	chr15:76350000-76350800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:76350000-76350800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:76350000-76351200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:76350000-76351200	Weak transcription	Pancreas	Pancrea
10	chr15:76350000-76351200	Weak transcription	Psoas Muscle	Psoas
11	chr15:76350000-76351200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:76350000-76351200	Enhancers	HMEC	breast
13	chr15:76350000-76351400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:76350200-76350600	Weak transcription	Brain Anterior Caudate	brain
15	chr15:76350200-76351000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
16	chr15:76350400-76350800	Enhancers	Brain Hippocampus Middle	brain
17	chr15:76350400-76351200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
18	chr15:76350400-76351800	Flanking Active TSS	GM12878-XiMat	blood

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