Variant report

Variant	rs558748776
Chromosome Location	chr1:241803504-241803505
allele	C/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	POLR2A	chr1:241803145-241804337	K562	blood:	n/a	n/a
2	POLR2A	chr1:241803069-241803761	H1-hESC	embryonic stem cell:	n/a	n/a
3	TCF3	chr1:241803342-241804033	GM12878	blood:	n/a	n/a
4	CTCF	chr1:241803188-241804110	K562	blood:	n/a	chr1:241803858-241803871
5	MAX	chr1:241802778-241804341	MCF-7	breast:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
6	TAF7	chr1:241803141-241803833	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr1:241802953-241804150	H1-hESC	embryonic stem cell:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
8	TEAD4	chr1:241803100-241803732	K562	blood:	n/a	n/a
9	POLR2A	chr1:241803293-241803737	GM12892	blood:	n/a	n/a
10	ELF1	chr1:241803467-241804037	K562	blood:	n/a	n/a
11	CREB1	chr1:241802910-241804233	HepG2	liver:	n/a	n/a
12	IRF1	chr1:241803238-241804049	K562	blood:	n/a	chr1:241803835-241803849
13	E2F4	chr1:241803201-241804785	K562	blood:	n/a	chr1:241803839-241803848 chr1:241804035-241804044
14	PML	chr1:241803367-241804095	K562	blood:	n/a	n/a
15	BHLHE40	chr1:241803135-241804489	K562	blood:	n/a	n/a
16	GTF2B	chr1:241803298-241803736	K562	blood:	n/a	n/a
17	POLR2A	chr1:241803114-241803760	K562	blood:	n/a	n/a
18	POLR2A	chr1:241803309-241803826	K562	blood:	n/a	n/a
19	POLR2A	chr1:241803306-241804070	ECC-1	luminal epithelium:	n/a	n/a
20	GABPA	chr1:241803238-241804151	K562	blood:	n/a	chr1:241803839-241803848
21	NFYA	chr1:241803493-241803782	Hela-S3	cervix:	n/a	n/a
22	MTA3	chr1:241803058-241803651	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:241803078-241804079	Hela-S3	cervix:	n/a	n/a
24	MAX	chr1:241803269-241805364	A549	lung:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
25	NR3C1	chr1:241803293-241804027	A549	lung:	n/a	n/a
26	ELF1	chr1:241803500-241804000	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:241802878-241804118	MCF-7	breast:	n/a	n/a
28	MAX	chr1:241803199-241805449	Hela-S3	cervix:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
29	CHD2	chr1:241803105-241805505	Hela-S3	cervix:	n/a	chr1:241803837-241803847
30	POLR2A	chr1:241803129-241804098	GM12878	blood:	n/a	n/a
31	CHD2	chr1:241803239-241804147	K562	blood:	n/a	chr1:241803837-241803847
32	POLR2A	chr1:241802883-241804030	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:241803080-241804080	HCT-116	colon:	n/a	n/a
34	POLR2A	chr1:241803121-241803754	GM12891	blood:	n/a	n/a
35	TCF12	chr1:241803313-241804123	ECC-1	luminal epithelium:	n/a	n/a
36	IRF1	chr1:241803180-241804081	K562	blood:	n/a	chr1:241803835-241803849
37	POLR2A	chr1:241803067-241804113	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr1:241802824-241803813	H1-hESC	embryonic stem cell:	n/a	n/a
39	POU2F2	chr1:241803446-241803692	GM12891	blood:	n/a	n/a
40	E2F1	chr1:241803118-241804102	Hela-S3	cervix:	n/a	chr1:241803839-241803848 chr1:241804035-241804044
41	POLR2A	chr1:241802685-241803962	IMR90	lung:	n/a	n/a
42	SIN3A	chr1:241802373-241803801	H1-hESC	embryonic stem cell:	n/a	n/a
43	E2F6	chr1:241802850-241804143	K562	blood:	n/a	chr1:241803839-241803848 chr1:241802963-241802975 chr1:241804035-241804044
44	POU2F2	chr1:241803424-241803677	GM12878	blood:	n/a	n/a
45	HDAC2	chr1:241803405-241803701	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:241803098-241804013	A549	lung:	n/a	n/a
47	TAF1	chr1:241803402-241804076	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr1:241803294-241804072	U87	brain:	n/a	n/a
49	TBP	chr1:241803265-241804928	HepG2	liver:	n/a	n/a
50	MAX	chr1:241803459-241804192	K562	blood:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057

No.	Distal block	Cell Line	Cell type
1	chr1:241802916..241803902-chr11:94800255..94801274,3	Hela-S3	cervix:
2	chr1:241693526..241696085-chr1:241801417..241805051,3	MCF-7	breast:
3	chr1:35324929..35325577-chr1:241803103..241803897,2	Hela-S3	cervix:
4	chr1:241799844..241805446-chr1:241909864..241915090,9	MCF-7	breast:
5	chr1:241801200..241805205-chr1:241910998..241914529,7	MCF-7	breast:
6	chr1:241802981..241803549-chr15:101419480..101420093,2	Hela-S3	cervix:
7	chr1:241803184..241804086-chr16:50186534..50187290,2	HCT-116	colon:
8	chr1:241803211..241803846-chr17:8338934..8339755,2	Hela-S3	cervix:
9	chr1:241803219..241803852-chr16:325251..325771,2	Hela-S3	cervix:
10	chr1:241797614..241799339-chr1:241801296..241804255,2	MCF-7	breast:
11	chr1:241803496..241804225-chr2:38978064..38978860,2	HCT-116	colon:
12	chr1:241802310..241805173-chr1:241993132..241995327,2	K562	blood:
13	chr1:241796724..241805103-chr1:242008052..242013159,15	K562	blood:
14	chr1:241799658..241805161-chr1:242010004..242013743,14	K562	blood:
15	chr1:113498019..113498730-chr1:241802542..241803505,2	Hela-S3	cervix:
16	chr1:241801957..241807032-chr1:241808533..241817679,11	K562	blood:
17	chr1:241803156..241803874-chr7:16685787..16686722,2	Hela-S3	cervix:

Variant related genes	Relation type
CHML	TF binding region
ENSG00000229022	Chromatin interaction
ENSG00000184254	Chromatin interaction
ENSG00000271885	Chromatin interaction
ENSG00000136261	Chromatin interaction
ENSG00000174371	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000162843	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000121274	Chromatin interaction
ENSG00000076344	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000166579	Chromatin interaction
ENSG00000117009	Chromatin interaction
ENSG00000163866	Chromatin interaction
ENSG00000203668	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	esv3399692	chr1:241802554-241805102	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
11	esv3427336	chr1:241802829-241804677	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	20 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	chr1:241799600-241804400	Active TSS	Brain Angular Gyrus	brain
2	chr1:241800400-241804200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:241800600-241804000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr1:241801200-241804000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:241801200-241804000	Active TSS	Placenta	Placenta
6	chr1:241801200-241804200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:241801200-241804200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:241801200-241804200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:241801200-241804200	Active TSS	Ovary	ovary
10	chr1:241801200-241804200	Active TSS	HSMM	muscle
11	chr1:241801400-241804000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:241801400-241804000	Active TSS	Colonic Mucosa	Colon
13	chr1:241801400-241804000	Active TSS	HSMMtube	muscle
14	chr1:241801600-241804000	Active TSS	Fetal Muscle Leg	muscle
15	chr1:241801600-241804000	Active TSS	A549	lung
16	chr1:241801600-241804000	Active TSS	GM12878-XiMat	blood
17	chr1:241801600-241804000	Active TSS	NHLF	lung
18	chr1:241801800-241803600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:241801800-241803800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:241801800-241803800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:241801800-241803800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:241801800-241803800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:241801800-241803800	Active TSS	Hela-S3	cervix
24	chr1:241801800-241804000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr1:241801800-241804000	Active TSS	H1 Cell Line	embryonic stem cell
26	chr1:241801800-241804000	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:241801800-241804000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:241801800-241804000	Active TSS	Fetal Intestine Large	intestine
29	chr1:241801800-241804000	Active TSS	Placenta Amnion	Placenta Amnion
30	chr1:241801800-241804200	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:241801800-241804200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:241801800-241804200	Active TSS	Aorta	Aorta
33	chr1:241802000-241803600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:241802000-241803800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:241802000-241803800	Active TSS	Primary B cells from peripheral blood	blood
36	chr1:241802000-241803800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:241802000-241803800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:241802000-241803800	Active TSS	HMEC	breast
39	chr1:241802000-241803800	Active TSS	NH-A	brain
40	chr1:241802000-241804000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:241802000-241804000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:241802000-241804000	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr1:241802000-241804000	Active TSS	NHEK	skin
44	chr1:241802000-241804200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:241802000-241804200	Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:241802000-241804200	Active TSS	Thymus	Thymus
47	chr1:241802000-241804400	Active TSS	Fetal Brain Female	brain
48	chr1:241802000-241804400	Active TSS	Fetal Kidney	kidney
49	chr1:241802000-241804600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:241802200-241804000	Active TSS	Primary hematopoietic stem cells short term culture	blood

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