Variant report

Variant	rs58260634
Chromosome Location	chr13:80059623-80059624
allele	A/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	TCF7L2	chr13:80059494-80059859	HEK293	kidney:	n/a	chr13:80059691-80059707 chr13:80059694-80059703 chr13:80059692-80059706 chr13:80059695-80059705
2	NR3C1	chr13:80059070-80059630	A549	lung:	n/a	n/a
3	CEBPB	chr13:80059235-80059937	K562	blood:	n/a	n/a
4	STAT3	chr13:80059095-80060085	MCF10A-Er-Src	breast:	n/a	chr13:80059487-80059498
5	RCOR1	chr13:80058976-80059978	Hela-S3	cervix:	n/a	n/a
6	MXI1	chr13:80059194-80059965	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr13:80058401-80060319	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr13:80059016-80059628	MCF10A-Er-Src	breast:	n/a	n/a
9	MAFK	chr13:80059370-80059634	K562	blood:	n/a	n/a
10	CEBPB	chr13:80059044-80059802	A549	lung:	n/a	n/a
11	SP1	chr13:80058925-80059646	A549	lung:	n/a	n/a
12	FOSL2	chr13:80059012-80059719	A549	lung:	n/a	n/a
13	POLR2A	chr13:80059000-80059624	Hela-S3	cervix:	n/a	n/a
14	STAT3	chr13:80059293-80059965	Hela-S3	cervix:	n/a	chr13:80059487-80059498
15	KAP1	chr13:80059205-80059805	U2OS	brain:	n/a	n/a
16	FOS	chr13:80059015-80059952	MCF10A-Er-Src	breast:	n/a	n/a
17	USF2	chr13:80059127-80059871	Hela-S3	cervix:	n/a	n/a
18	NR3C1	chr13:80059030-80059761	A549	lung:	n/a	n/a
19	MYC	chr13:80058597-80059952	MCF10A-Er-Src	breast:	n/a	n/a
20	MAFF	chr13:80059389-80059811	K562	blood:	n/a	n/a
21	TCF7L2	chr13:80059050-80060060	Hela-S3	cervix:	n/a	chr13:80059691-80059707 chr13:80059694-80059703 chr13:80059692-80059706 chr13:80059695-80059705
22	CEBPB	chr13:80059105-80059877	A549	lung:	n/a	n/a
23	RFX5	chr13:80058960-80059918	Hela-S3	cervix:	n/a	n/a
24	MAFK	chr13:80059050-80059700	HepG2	liver:	n/a	n/a
25	GTF2F1	chr13:80059113-80059804	Hela-S3	cervix:	n/a	n/a
26	ELK1	chr13:80059081-80059931	Hela-S3	cervix:	n/a	n/a
27	MAFK	chr13:80059056-80059694	HepG2	liver:	n/a	n/a
28	RAD21	chr13:80059142-80059881	Hela-S3	cervix:	n/a	n/a
29	EP300	chr13:80058881-80059743	A549	lung:	n/a	n/a
30	STAT3	chr13:80059021-80059819	MCF10A-Er-Src	breast:	n/a	chr13:80059487-80059498
31	EP300	chr13:80059048-80060156	Hela-S3	cervix:	n/a	n/a
32	CEBPB	chr13:80059101-80059914	HepG2	liver:	n/a	n/a
33	JUND	chr13:80059053-80059664	HepG2	liver:	n/a	n/a
34	BRCA1	chr13:80058879-80059947	Hela-S3	cervix:	n/a	n/a
35	ARID3A	chr13:80059079-80059687	HepG2	liver:	n/a	n/a
36	POLR2A	chr13:80058362-80061635	MCF10A-Er-Src	breast:	n/a	n/a
37	NR3C1	chr13:80059115-80059684	A549	lung:	n/a	n/a
38	EP300	chr13:80058882-80059687	A549	lung:	n/a	n/a
39	MXI1	chr13:80059150-80059711	HepG2	liver:	n/a	n/a
40	MYC	chr13:80058986-80059892	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr13:80058816-80059894	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr13:80059171-80059632	K562	blood:	n/a	n/a
43	SP1	chr13:80059182-80059679	HepG2	liver:	n/a	n/a
44	MAX	chr13:80059083-80059886	Hela-S3	cervix:	n/a	n/a
45	TCF7L2	chr13:80059239-80060002	Hela-S3	cervix:	n/a	chr13:80059691-80059707 chr13:80059694-80059703 chr13:80059692-80059706 chr13:80059695-80059705
46	MAFF	chr13:80059035-80059686	HepG2	liver:	n/a	n/a
47	SMC3	chr13:80059098-80060032	Hela-S3	cervix:	n/a	n/a
48	MAX	chr13:80059108-80059911	Hela-S3	cervix:	n/a	n/a
49	TCF12	chr13:80058967-80059689	A549	lung:	n/a	n/a
50	MAFK	chr13:80059029-80059693	IMR90	lung:	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: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs17071373	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071564	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071576	1.00[AMR][1000 genomes]
rs17071581	1.00[AMR][1000 genomes]
rs17071592	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071596	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071599	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071601	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071609	1.00[AMR][1000 genomes]
rs17071610	1.00[AMR][1000 genomes]
rs17071613	1.00[AMR][1000 genomes]
rs17071624	1.00[AMR][1000 genomes]
rs55887763	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56737007	1.00[AMR][1000 genomes]
rs56823234	1.00[AMR][1000 genomes]
rs57066341	1.00[AMR][1000 genomes]
rs57068944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57560404	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57603166	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57615648	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57863151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58006070	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58088304	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58322995	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58325260	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58379158	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58833188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58930697	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59105864	1.00[AMR][1000 genomes]
rs59232955	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59245717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59331936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59604922	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59945183	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60119719	0.99[AFR][1000 genomes]
rs60183984	1.00[AMR][1000 genomes]
rs60240323	1.00[AMR][1000 genomes]
rs60575675	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60827595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61216430	1.00[AMR][1000 genomes]
rs61368443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61464969	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7139938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7323341	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7324225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7328479	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7332059	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7332241	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7337248	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73548917	1.00[AMR][1000 genomes]
rs73548923	1.00[AMR][1000 genomes]
rs73548924	1.00[AMR][1000 genomes]
rs73548926	1.00[AMR][1000 genomes]
rs73548938	1.00[AMR][1000 genomes]
rs73548941	1.00[AMR][1000 genomes]
rs73548942	1.00[AMR][1000 genomes]
rs73549001	1.00[AMR][1000 genomes]
rs73551505	1.00[AMR][1000 genomes]
rs73551522	1.00[AMR][1000 genomes]
rs73551530	1.00[AMR][1000 genomes]
rs73551537	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551547	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551548	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551551	1.00[AMR][1000 genomes]
rs73551555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551567	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551569	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551570	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551575	1.00[AMR][1000 genomes]
rs73551578	1.00[AMR][1000 genomes]
rs73551581	1.00[AMR][1000 genomes]
rs73551583	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551589	1.00[AMR][1000 genomes]
rs73551592	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551599	1.00[AMR][1000 genomes]
rs73553407	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553414	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553416	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553419	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553423	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553442	1.00[AMR][1000 genomes]
rs73553454	1.00[AMR][1000 genomes]
rs73553459	1.00[AMR][1000 genomes]
rs73564691	1.00[AMR][1000 genomes]
rs73566444	1.00[AMR][1000 genomes]
rs74098262	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74100736	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7983904	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7988143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7990488	0.96[AFR][1000 genomes];1.00[AMR][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:86 , 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	chr13:80058200-80059800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr13:80058400-80059800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr13:80058400-80059800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr13:80058400-80060200	Flanking Active TSS	A549	lung
30	chr13:80058400-80060200	Transcr. at gene 5' and 3'	Dnd41	blood
31	chr13:80058400-80061400	Enhancers	Stomach Mucosa	stomach
32	chr13:80058400-80062600	Enhancers	Fetal Intestine Small	intestine
33	chr13:80058600-80060200	Enhancers	NHLF	lung
34	chr13:80058600-80061200	Enhancers	NHDF-Ad	bronchial
35	chr13:80058600-80065800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr13:80058800-80059800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr13:80058800-80059800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:80058800-80059800	Enhancers	Adipose Nuclei	Adipose
39	chr13:80058800-80059800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr13:80058800-80059800	Flanking Active TSS	Hela-S3	cervix
41	chr13:80058800-80060600	Active TSS	Duodenum Mucosa	Duodenum
42	chr13:80058800-80060600	Flanking Active TSS	NHEK	skin
43	chr13:80059000-80059800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr13:80059000-80060000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr13:80059000-80060000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:80059000-80060200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr13:80059000-80060200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr13:80059000-80077200	Weak transcription	Small Intestine	intestine
49	chr13:80059200-80059800	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr13:80059200-80059800	Bivalent Enhancer	Primary T cells from cord blood	blood

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