Variant report

Variant	rs1498196
Chromosome Location	chr15:76350952-76350953
allele	C/T
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

No.	Distal block	Cell Line	Cell type
1	chr15:76350662..76351851-chr15:76431467..76432496,4	MCF-7	breast:
2	chr15:76134992..76136572-chr15:76350644..76353343,2	MCF-7	breast:
3	chr15:76195094..76197177-chr15:76350015..76352498,2	K562	blood:
4	chr15:76350898..76351807-chr15:76431306..76432503,7	MCF-7	breast:
5	chr15:76341281..76343239-chr15:76349906..76351616,2	MCF-7	breast:

Variant related genes	Relation type
C15orf27	TF binding region
NRG4	TF binding region
ENSG00000140367	Chromatin interaction
ENSG00000167196	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:173)

rs_ID	r²[population]
rs1039547	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs13379955	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1394122	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1498197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1498198	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1503955	1.00[CEU][hapmap];0.81[YRI][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	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[YRI][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	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];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs2405578	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs2441928	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2454209	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2454210	1.00[CEU][hapmap]
rs2454212	0.80[ASW][hapmap];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];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs2460795	1.00[EUR][1000 genomes]
rs2460796	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs2460801	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	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2648437	1.00[CEU][hapmap];1.00[TSI][hapmap];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];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs2959848	0.89[MKK][hapmap]
rs2959851	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];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[ASW][hapmap];1.00[CEU][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs334941	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs334951	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335673	1.00[EUR][1000 genomes]
rs335674	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs335675	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs335676	0.85[EUR][1000 genomes]
rs335678	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs335679	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs335683	1.00[EUR][1000 genomes]
rs335684	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs335687	1.00[CEU][hapmap];0.81[YRI][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];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs335725	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs335726	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs335728	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs335729	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs335730	1.00[EUR][1000 genomes]
rs335731	1.00[EUR][1000 genomes]
rs335732	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs335733	1.00[CEU][hapmap];0.81[YRI][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	1.00[EUR][1000 genomes]
rs74024030	1.00[EUR][1000 genomes]
rs74024032	1.00[EUR][1000 genomes]
rs74024035	1.00[EUR][1000 genomes]
rs74024038	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];0.81[YRI][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];0.81[YRI][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];1.00[EUR][1000 genomes]
rs8038729	0.92[EUR][1000 genomes]
rs9672219	1.00[EUR][1000 genomes]
rs974718	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3425731	chr15:76350922-76353470	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1498196	FBXO22	cis	lymphoblastoid	seeQTL
rs1498196	FBXO22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 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	chr15:76349600-76351400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:76349800-76351000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:76349800-76351200	Active TSS	Brain Angular Gyrus	brain
5	chr15:76350000-76351200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:76350000-76351200	Weak transcription	Pancreas	Pancrea
7	chr15:76350000-76351200	Weak transcription	Psoas Muscle	Psoas
8	chr15:76350000-76351200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:76350000-76351200	Enhancers	HMEC	breast
10	chr15:76350000-76351400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:76350200-76351000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
12	chr15:76350400-76351200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
13	chr15:76350400-76351800	Flanking Active TSS	GM12878-XiMat	blood
14	chr15:76350600-76351000	Bivalent Enhancer	A549	lung
15	chr15:76350600-76351000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
16	chr15:76350600-76351400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr15:76350600-76351400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr15:76350800-76351000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
19	chr15:76350800-76351000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
20	chr15:76350800-76351000	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr15:76350800-76351200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr15:76350800-76351200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr15:76350800-76351200	Bivalent Enhancer	Primary B cells from cord blood	blood
24	chr15:76350800-76351200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:76350800-76351200	Active TSS	Brain Cingulate Gyrus	brain
26	chr15:76350800-76351200	Active TSS	Brain Hippocampus Middle	brain
27	chr15:76350800-76351200	Bivalent Enhancer	Fetal Kidney	kidney
28	chr15:76350800-76351200	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr15:76350800-76351400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
30	chr15:76350800-76353200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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