Variant report

Variant	rs17071499
Chromosome Location	chr13:80059878-80059879
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	CEBPB	chr13:80059235-80059937	K562	blood:	n/a	n/a
2	STAT3	chr13:80059095-80060085	MCF10A-Er-Src	breast:	n/a	chr13:80059487-80059498
3	RCOR1	chr13:80058976-80059978	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr13:80059194-80059965	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr13:80058401-80060319	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr13:80059293-80059965	Hela-S3	cervix:	n/a	chr13:80059487-80059498
7	FOS	chr13:80059015-80059952	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr13:80058597-80059952	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF7L2	chr13:80059050-80060060	Hela-S3	cervix:	n/a	chr13:80059691-80059707 chr13:80059694-80059703 chr13:80059692-80059706 chr13:80059695-80059705
10	RFX5	chr13:80058960-80059918	Hela-S3	cervix:	n/a	n/a
11	ELK1	chr13:80059081-80059931	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr13:80059142-80059881	Hela-S3	cervix:	n/a	n/a
13	EP300	chr13:80059048-80060156	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr13:80059101-80059914	HepG2	liver:	n/a	n/a
15	BRCA1	chr13:80058879-80059947	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr13:80058362-80061635	MCF10A-Er-Src	breast:	n/a	n/a
17	MYC	chr13:80058986-80059892	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr13:80058816-80059894	Hela-S3	cervix:	n/a	n/a
19	MAX	chr13:80059083-80059886	Hela-S3	cervix:	n/a	n/a
20	TCF7L2	chr13:80059239-80060002	Hela-S3	cervix:	n/a	chr13:80059691-80059707 chr13:80059694-80059703 chr13:80059692-80059706 chr13:80059695-80059705
21	SMC3	chr13:80059098-80060032	Hela-S3	cervix:	n/a	n/a
22	MAX	chr13:80059108-80059911	Hela-S3	cervix:	n/a	n/a
23	SPI1	chr13:80059260-80059971	HL-60	blood:	n/a	n/a
24	FOS	chr13:80058981-80059968	MCF10A-Er-Src	breast:	n/a	n/a
25	CEBPB	chr13:80059000-80059984	Hela-S3	cervix:	n/a	n/a
26	CEBPB	chr13:80059052-80059948	IMR90	lung:	n/a	n/a
27	TBP	chr13:80059075-80059930	Hela-S3	cervix:	n/a	n/a
28	MAFK	chr13:80059059-80060091	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:80057193..80059999-chr13:80114272..80116741,2	K562	blood:

Variant related genes	Relation type
NDFIP2-AS1	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10492579	0.92[EUR][1000 genomes]
rs10507898	1.00[CEU][hapmap]
rs10507899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1335372	0.82[EUR][1000 genomes]
rs1335373	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1335374	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1414157	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17071233	1.00[CEU][hapmap]
rs17071247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17071257	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs17071385	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17071415	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17071532	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17071549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17071558	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17071566	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17071574	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17071585	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17071627	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17071632	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs41288268	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56711390	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs57032852	0.92[EUR][1000 genomes]
rs57544957	0.80[EUR][1000 genomes]
rs57929179	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58056613	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58069884	0.89[EUR][1000 genomes]
rs58264675	0.82[EUR][1000 genomes]
rs58406632	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs59165380	0.82[EUR][1000 genomes]
rs59381369	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59755477	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59773478	0.80[EUR][1000 genomes]
rs59783325	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60126328	0.84[EUR][1000 genomes]
rs61318325	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61676417	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6563107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs6563117	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7139902	0.82[EUR][1000 genomes]
rs7317409	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7317511	0.92[EUR][1000 genomes]
rs7318854	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7318984	0.84[EUR][1000 genomes]
rs7327148	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7329633	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7330804	0.84[EUR][1000 genomes]
rs7331979	1.00[CEU][hapmap]
rs7335191	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7338043	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73548948	0.82[EUR][1000 genomes]
rs73548951	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73548955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551558	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551595	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73551596	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73551597	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73551601	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73551602	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73553403	0.92[EUR][1000 genomes]
rs73553418	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73553424	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73553431	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73553447	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73553448	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73553473	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73553481	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73553499	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs73555409	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73555411	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs73555415	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs73566422	0.80[EUR][1000 genomes]
rs73566424	0.80[EUR][1000 genomes]
rs73566435	0.80[EUR][1000 genomes]
rs73566454	0.80[EUR][1000 genomes]
rs7491258	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7981574	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7984159	1.00[EUR][1000 genomes]
rs7984598	0.96[EUR][1000 genomes]
rs7985220	0.89[EUR][1000 genomes]
rs7985697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7990190	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7990464	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7992181	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7997554	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7998452	0.92[EUR][1000 genomes]
rs8000870	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80056200-80060600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:80056200-80060800	Weak transcription	Gastric	stomach
3	chr13:80056200-80063200	Weak transcription	Left Ventricle	heart
4	chr13:80056200-80066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:80056200-80066600	Weak transcription	Psoas Muscle	Psoas
6	chr13:80056200-80077400	Weak transcription	Right Ventricle	heart
7	chr13:80056600-80064200	Weak transcription	Placenta	Placenta
8	chr13:80056800-80061200	Enhancers	Fetal Heart	heart
9	chr13:80056800-80064000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr13:80056800-80064400	Weak transcription	Fetal Stomach	stomach
11	chr13:80056800-80065800	Weak transcription	Fetal Muscle Leg	muscle
12	chr13:80057000-80063600	Weak transcription	Right Atrium	heart
13	chr13:80057000-80066200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:80057200-80060600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:80057400-80060800	Enhancers	HSMM	muscle
16	chr13:80057400-80063400	Weak transcription	GM12878-XiMat	blood
17	chr13:80057400-80064600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:80057600-80060000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr13:80057600-80061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:80057600-80065400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr13:80057600-80065600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:80057800-80064600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:80057800-80064600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr13:80058000-80060200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr13:80058000-80065400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr13:80058400-80060200	Flanking Active TSS	A549	lung
27	chr13:80058400-80060200	Transcr. at gene 5' and 3'	Dnd41	blood
28	chr13:80058400-80061400	Enhancers	Stomach Mucosa	stomach
29	chr13:80058400-80062600	Enhancers	Fetal Intestine Small	intestine
30	chr13:80058600-80060200	Enhancers	NHLF	lung
31	chr13:80058600-80061200	Enhancers	NHDF-Ad	bronchial
32	chr13:80058600-80065800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr13:80058800-80060600	Active TSS	Duodenum Mucosa	Duodenum
34	chr13:80058800-80060600	Flanking Active TSS	NHEK	skin
35	chr13:80059000-80060000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr13:80059000-80060000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr13:80059000-80060200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr13:80059000-80060200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr13:80059000-80077200	Weak transcription	Small Intestine	intestine
40	chr13:80059200-80060000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr13:80059200-80060000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr13:80059200-80060200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr13:80059200-80060200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr13:80059400-80060000	Flanking Active TSS	HMEC	breast
45	chr13:80059400-80060000	Flanking Active TSS	NH-A	brain
46	chr13:80059400-80060200	Flanking Active TSS	Osteobl	bone
47	chr13:80059400-80061600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr13:80059400-80062200	Enhancers	Liver	Liver
49	chr13:80059400-80064800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr13:80059400-80066400	Weak transcription	Fetal Thymus	thymus

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