Variant report

Variant	rs58024885
Chromosome Location	chr1:174129231-174129232
allele	A/C
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	BHLHE40	chr1:174127962-174129636	K562	blood:	n/a	chr1:174128488-174128504
2	EBF1	chr1:174129019-174129259	GM12878	blood:	n/a	n/a
3	MAX	chr1:174128221-174129324	K562	blood:	n/a	n/a
4	SPI1	chr1:174129153-174129338	K562	blood:	n/a	chr1:174129257-174129270 chr1:174129259-174129266
5	YY1	chr1:174128986-174129279	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:174127564-174130052	Raji	blood:	n/a	n/a
7	NR2F2	chr1:174127922-174129594	K562	blood:	n/a	n/a
8	E2F4	chr1:174128148-174129668	K562	blood:	n/a	chr1:174128487-174128497 chr1:174129032-174129041 chr1:174128385-174128396
9	E2F1	chr1:174128168-174129464	Hela-S3	cervix:	n/a	chr1:174128487-174128497 chr1:174129032-174129041
10	POLR2A	chr1:174128218-174129319	H1-neurons	neurons:	n/a	n/a
11	BACH1	chr1:174129084-174129332	H1-hESC	embryonic stem cell:	n/a	n/a
12	EGR1	chr1:174128014-174129318	HCT-116	colon:	n/a	chr1:174128529-174128538 chr1:174129031-174129041 chr1:174128484-174128498 chr1:174128953-174128966
13	POLR2A	chr1:174127563-174129733	GM12878	blood:	n/a	n/a
14	SMC3	chr1:174128188-174129645	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:174127613-174129697	GM15510	blood:	n/a	n/a
16	CTBP2	chr1:174128325-174129672	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3AK20	chr1:174127618-174129756	MCF-7	breast:	n/a	n/a
18	POLR2A	chr1:174127680-174129746	PBDE	blood:	n/a	n/a
19	RELA	chr1:174127667-174129632	GM10847	blood:	n/a	chr1:174129361-174129370 chr1:174129361-174129370
20	ZNF143	chr1:174128257-174129571	Hela-S3	cervix:	n/a	chr1:174128491-174128501 chr1:174128771-174128781 chr1:174129409-174129427
21	RELA	chr1:174127358-174129544	GM19193	blood:	n/a	chr1:174129361-174129370 chr1:174129361-174129370
22	ETS1	chr1:174128230-174129632	K562	blood:	n/a	chr1:174128756-174128763 chr1:174129030-174129041 chr1:174128486-174128497 chr1:174128489-174128500
23	POLR2A	chr1:174128230-174129757	HepG2	liver:	n/a	n/a
24	RELA	chr1:174126135-174129608	GM18505	blood:	n/a	chr1:174129361-174129370 chr1:174129361-174129370
25	CTCF	chr1:174129120-174129270	GM12873	blood:	n/a	chr1:174129146-174129159
26	MEF2A	chr1:174128164-174129579	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:174128115-174129623	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:174127833-174129498	HepG2	liver:	n/a	n/a
29	ELK1	chr1:174129201-174129705	K562	blood:	n/a	n/a
30	SIN3AK20	chr1:174128200-174129646	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr1:174128141-174129845	MCF10A-Er-Src	breast:	n/a	n/a
32	SIN3A	chr1:174127905-174129648	H1-hESC	embryonic stem cell:	n/a	chr1:174128772-174128781
33	POLR2A	chr1:174126096-174130044	GM12891	blood:	n/a	n/a
34	POLR2A	chr1:174128511-174129568	IMR90	lung:	n/a	n/a
35	TBP	chr1:174128104-174129373	H1-hESC	embryonic stem cell:	n/a	n/a
36	HA-E2F1	chr1:174127857-174129602	MCF-7	breast:	n/a	chr1:174128487-174128497 chr1:174129032-174129041
37	ELF1	chr1:174127976-174129578	GM12878	blood:	n/a	chr1:174128771-174128783 chr1:174128486-174128495 chr1:174128489-174128498
38	BCLAF1	chr1:174127981-174129420	K562	blood:	n/a	chr1:174128435-174128444 chr1:174128489-174128502 chr1:174128486-174128499 chr1:174128958-174128971 chr1:174128770-174128783 chr1:174128485-174128494 chr1:174128488-174128497 chr1:174128832-174128845
39	POLR2A	chr1:174127926-174129757	K562	blood:	n/a	n/a
40	ZEB1	chr1:174128478-174129317	GM12878	blood:	n/a	n/a
41	NR2F2	chr1:174128183-174129465	MCF-7	breast:	n/a	n/a
42	POLR2A	chr1:174127434-174129743	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:174129030-174129598	GM12891	blood:	n/a	n/a
44	TAF1	chr1:174128185-174129305	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr1:174129146-174129353	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:174128039-174129442	K562	blood:	n/a	n/a
47	MAX	chr1:174128103-174129740	K562	blood:	n/a	n/a
48	EP300	chr1:174129052-174129675	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:174128233-174129319	Gliobla	brain:	n/a	n/a
50	POLR2A	chr1:174128233-174129374	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173791511..173794568-chr1:174127376..174130126,4	K562	blood:
2	chr1:173990484..173993026-chr1:174127463..174130354,3	K562	blood:
3	chr1:90460484..90461049-chr1:174128407..174129288,2	Hela-S3	cervix:
4	chr1:174128812..174129312-chr19:47291339..47292302,2	NB4	blood:
5	chr1:173990191..173994093-chr1:174126470..174130234,3	MCF-7	breast:
6	chr1:174128312..174130705-chr1:174967510..174969928,2	K562	blood:
7	chr1:174128367..174129924-chr16:2014665..2017256,2	K562	blood:
8	chr1:173837020..173839325-chr1:174127377..174129524,4	K562	blood:
9	chr1:173835391..173837802-chr1:174127164..174130207,3	MCF-7	breast:
10	chr1:173836251..173838308-chr1:174127483..174129757,2	MCF-7	breast:
11	chr1:173991432..173994922-chr1:174124746..174129302,4	K562	blood:
12	chr1:173445824..173447952-chr1:174128991..174131620,2	K562	blood:
13	chr1:173835729..173840438-chr1:174127915..174131019,7	K562	blood:
14	chr1:174128312..174129852-chr1:174967356..174969010,2	K562	blood:

Variant related genes	Relation type
ENSG00000227373	TF binding region
ENSG00000234741	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000179580	Chromatin interaction
ENSG00000255198	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000162664	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000105281	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000140988	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16846660	1.00[AMR][1000 genomes]
rs16846662	1.00[AMR][1000 genomes]
rs16846681	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846728	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846747	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846840	0.86[AFR][1000 genomes]
rs2095986	0.90[AFR][1000 genomes]
rs41266044	0.84[AFR][1000 genomes]
rs41511350	0.90[AFR][1000 genomes]
rs4518972	0.88[AFR][1000 genomes]
rs60141888	0.90[AFR][1000 genomes]
rs60839216	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61635459	0.86[AFR][1000 genomes]
rs6687429	1.00[AMR][1000 genomes]
rs7339904	0.90[AFR][1000 genomes]
rs7550085	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174127600-174129400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:174127600-174129400	Active TSS	Fetal Stomach	stomach
3	chr1:174127600-174129600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:174127600-174129600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:174127600-174129600	Active TSS	Rectal Smooth Muscle	rectum
6	chr1:174127600-174129800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:174127600-174129800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:174127600-174129800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:174127600-174129800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr1:174127600-174130000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr1:174127600-174130000	Active TSS	Colonic Mucosa	Colon
12	chr1:174127600-174130000	Active TSS	NHDF-Ad	bronchial
13	chr1:174127600-174130000	Active TSS	NHLF	lung
14	chr1:174127600-174130200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:174127800-174129400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr1:174127800-174129400	Active TSS	Right Ventricle	heart
17	chr1:174127800-174129400	Active TSS	Thymus	Thymus
18	chr1:174127800-174129400	Active TSS	A549	lung
19	chr1:174127800-174129600	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:174127800-174129600	Active TSS	Stomach Mucosa	stomach
21	chr1:174127800-174129800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:174127800-174129800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:174127800-174129800	Active TSS	Aorta	Aorta
24	chr1:174127800-174129800	Active TSS	Brain Substantia Nigra	brain
25	chr1:174127800-174129800	Active TSS	Psoas Muscle	Psoas
26	chr1:174127800-174129800	Active TSS	HSMM	muscle
27	chr1:174127800-174129800	Active TSS	HSMMtube	muscle
28	chr1:174127800-174130000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:174127800-174130000	Active TSS	Fetal Intestine Large	intestine
30	chr1:174127800-174130000	Active TSS	Placenta Amnion	Placenta Amnion
31	chr1:174127800-174130200	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr1:174128000-174129400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:174128000-174129400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:174128000-174129400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:174128000-174129400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:174128000-174129400	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr1:174128000-174129400	Active TSS	Brain Cingulate Gyrus	brain
38	chr1:174128000-174129400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:174128000-174129400	Active TSS	Esophagus	oesophagus
40	chr1:174128000-174129400	Active TSS	Fetal Brain Female	brain
41	chr1:174128000-174129400	Active TSS	Lung	lung
42	chr1:174128000-174129400	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr1:174128000-174129400	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr1:174128000-174129600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:174128000-174129600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:174128000-174129600	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr1:174128000-174129600	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr1:174128000-174129600	Active TSS	Pancreas	Pancrea
49	chr1:174128000-174129600	Active TSS	Small Intestine	intestine
50	chr1:174128000-174129600	Bivalent/Poised TSS	HepG2	liver

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