Variant report

Variant	rs59250599
Chromosome Location	chr1:94147552-94147553
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	POLR2A	chr1:94144711-94147850	SK-N-SH	brain:	n/a	n/a
2	KAP1	chr1:94147527-94147727	U2OS	brain:	n/a	n/a
3	E2F6	chr1:94147247-94147622	H1-hESC	embryonic stem cell:	n/a	chr1:94147399-94147408
4	E2F4	chr1:94147307-94147811	MCF10A-Er-Src	breast:	n/a	chr1:94147399-94147408
5	POLR2A	chr1:94145966-94147845	GM18505	blood:	n/a	n/a
6	TAF1	chr1:94146220-94147761	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:94147064-94147729	GM12892	blood:	n/a	n/a
8	FOS	chr1:94147352-94147652	HUVEC	blood vessel:	n/a	chr1:94147594-94147603
9	POLR2A	chr1:94147143-94147649	PANC-1	pancreas:	n/a	n/a
10	POU2F2	chr1:94147303-94147610	GM12891	blood:	n/a	chr1:94147357-94147369
11	REST	chr1:94147153-94147617	SK-N-SH	brain:	n/a	chr1:94147368-94147381 chr1:94147377-94147390 chr1:94147374-94147392
12	MAX	chr1:94145972-94147860	A549	lung:	n/a	n/a
13	SIN3A	chr1:94146116-94147796	H1-hESC	embryonic stem cell:	n/a	chr1:94146813-94146826 chr1:94146820-94146829 chr1:94147370-94147381 chr1:94147368-94147381
14	GATA3	chr1:94144424-94147772	SK-N-SH	brain:	n/a	chr1:94144834-94144846 chr1:94144821-94144828 chr1:94145364-94145374 chr1:94144837-94144844 chr1:94144835-94144845 chr1:94145364-94145373 chr1:94147594-94147604 chr1:94144817-94144833 chr1:94144837-94144844 chr1:94144821-94144828 chr1:94144817-94144833 chr1:94145122-94145131 chr1:94144821-94144828 chr1:94145019-94145027 chr1:94144837-94144844
15	RAD21	chr1:94147148-94147679	ECC-1	luminal epithelium:	n/a	chr1:94147371-94147385 chr1:94147373-94147387
16	TCF12	chr1:94147267-94147672	GM12878	blood:	n/a	n/a
17	ZNF143	chr1:94147264-94147628	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr1:94147166-94147553	IMR90	lung:	n/a	chr1:94147374-94147387 chr1:94147374-94147387
19	REST	chr1:94147239-94147649	SK-N-SH	brain:	n/a	chr1:94147368-94147381 chr1:94147377-94147390 chr1:94147374-94147392
20	PAX5	chr1:94147147-94147561	GM12892	blood:	n/a	n/a
21	RAD21	chr1:94147235-94147554	SK-N-SH_RA	brain:	n/a	chr1:94147371-94147385 chr1:94147373-94147387
22	POLR2A	chr1:94147025-94147618	A549	lung:	n/a	n/a
23	POLR2A	chr1:94147158-94147765	Raji	blood:	n/a	n/a
24	MAZ	chr1:94145815-94147841	Hela-S3	cervix:	n/a	n/a
25	SP1	chr1:94147288-94147746	A549	lung:	n/a	chr1:94147356-94147370 chr1:94147444-94147453 chr1:94147443-94147455
26	RCOR1	chr1:94147284-94147557	K562	blood:	n/a	n/a
27	POLR2A	chr1:94145711-94147828	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:94147441-94147610	GM12878	blood:	n/a	n/a
29	HA-E2F1	chr1:94146826-94147574	Hela-S3	cervix:	n/a	chr1:94147096-94147106 chr1:94146969-94146978 chr1:94147399-94147408
30	POLR2A	chr1:94146207-94147768	HUVEC	blood vessel:	n/a	n/a
31	MAX	chr1:94145818-94147792	Hela-S3	cervix:	n/a	n/a
32	CREB1	chr1:94147017-94147593	A549	lung:	n/a	n/a
33	TAF1	chr1:94147061-94147942	ECC-1	luminal epithelium:	n/a	n/a
34	UBTF	chr1:94147047-94147596	K562	blood:	n/a	n/a
35	CTCF	chr1:94147251-94147605	A549	lung:	n/a	chr1:94147374-94147387 chr1:94147374-94147387
36	TCF12	chr1:94146940-94147744	ECC-1	luminal epithelium:	n/a	chr1:94147700-94147707
37	ZNF143	chr1:94147127-94147601	Hela-S3	cervix:	n/a	n/a
38	CEBPB	chr1:94147278-94147808	Hela-S3	cervix:	n/a	n/a
39	ELK1	chr1:94147248-94147633	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr1:94147178-94147602	H1-hESC	embryonic stem cell:	n/a	chr1:94147371-94147385 chr1:94147373-94147387
41	SMARCC1	chr1:94145728-94147882	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:94147058-94147812	GM12892	blood:	n/a	n/a
43	MAZ	chr1:94146986-94147567	K562	blood:	n/a	n/a
44	TAF1	chr1:94147291-94147639	SK-N-SH	brain:	n/a	n/a
45	BACH1	chr1:94147306-94147696	H1-hESC	embryonic stem cell:	n/a	n/a
46	TAF1	chr1:94147244-94147796	A549	lung:	n/a	n/a
47	RAD21	chr1:94147058-94147594	HepG2	liver:	n/a	chr1:94147371-94147385 chr1:94147373-94147387
48	CTCF	chr1:94147255-94147604	K562	blood:	n/a	chr1:94147374-94147387 chr1:94147374-94147387
49	RAD21	chr1:94147178-94147737	IMR90	lung:	n/a	chr1:94147371-94147385 chr1:94147373-94147387
50	POLR2A	chr1:94146913-94147858	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94146501..94148043-chr1:94311466..94313377,2	MCF-7	breast:
2	chr1:93913059..93915471-chr1:94146480..94149352,2	MCF-7	breast:
3	chr1:94145898..94148493-chr1:94311257..94313086,3	MCF-7	breast:
4	chr1:94147125..94147625-chr12:92539531..92540032,2	Hela-S3	cervix:

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000260464	Chromatin interaction
ENSG00000133639	Chromatin interaction
ENSG00000137942	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000245904	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13373766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17109954	1.00[EUR][1000 genomes]
rs17110016	1.00[EUR][1000 genomes]
rs35555794	1.00[EUR][1000 genomes]
rs55670441	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55742446	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55936005	1.00[AMR][1000 genomes]
rs57291093	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58351576	1.00[EUR][1000 genomes]
rs60032869	1.00[EUR][1000 genomes]
rs60046384	1.00[EUR][1000 genomes]
rs60383814	1.00[EUR][1000 genomes]
rs61215181	1.00[EUR][1000 genomes]
rs6664053	1.00[EUR][1000 genomes]
rs6682265	1.00[EUR][1000 genomes]
rs6687167	1.00[EUR][1000 genomes]
rs74101588	1.00[EUR][1000 genomes]
rs74101589	1.00[EUR][1000 genomes]
rs74101603	1.00[EUR][1000 genomes]
rs74101657	1.00[AMR][1000 genomes]
rs74101663	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101667	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101669	1.00[EUR][1000 genomes]
rs74101670	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74104033	1.00[EUR][1000 genomes]
rs7525388	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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94144400-94148200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:94144600-94148400	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:94145000-94148000	Active TSS	Brain Anterior Caudate	brain
4	chr1:94145200-94148000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:94145400-94147600	Active TSS	Muscle Satellite Cultured Cells	--
6	chr1:94145400-94147800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:94145400-94148400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:94145400-94148400	Active TSS	HSMM	muscle
9	chr1:94145600-94147600	Active TSS	Fetal Kidney	kidney
10	chr1:94145600-94147800	Active TSS	NHDF-Ad	bronchial
11	chr1:94145600-94148000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:94145600-94148200	Active TSS	A549	lung
13	chr1:94145800-94147600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr1:94145800-94147600	Active TSS	Hela-S3	cervix
15	chr1:94145800-94148000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:94145800-94148000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:94145800-94148000	Bivalent/Poised TSS	Fetal Brain Female	brain
18	chr1:94145800-94148000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:94145800-94148200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:94146000-94147600	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr1:94146000-94147600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr1:94146000-94147800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr1:94146000-94147800	Active TSS	Ovary	ovary
24	chr1:94146000-94148000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:94146000-94148200	Active TSS	Brain Angular Gyrus	brain
26	chr1:94146200-94147600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:94146200-94147600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:94146200-94147600	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr1:94146200-94147600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:94146200-94147600	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr1:94146200-94147600	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr1:94146200-94147600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:94146200-94147600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:94146200-94147600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:94146200-94147600	Active TSS	Colon Smooth Muscle	Colon
36	chr1:94146200-94147600	Active TSS	Duodenum Mucosa	Duodenum
37	chr1:94146200-94147600	Active TSS	Placenta	Placenta
38	chr1:94146200-94147600	Active TSS	Lung	lung
39	chr1:94146200-94147800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:94146200-94147800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:94146200-94147800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:94146200-94147800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:94146200-94147800	Active TSS	Aorta	Aorta
44	chr1:94146200-94147800	Flanking Active TSS	Liver	Liver
45	chr1:94146200-94147800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
46	chr1:94146200-94147800	Active TSS	Brain Substantia Nigra	brain
47	chr1:94146200-94147800	Active TSS	Gastric	stomach
48	chr1:94146200-94147800	Active TSS	HMEC	breast
49	chr1:94146200-94147800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr1:94146200-94148000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links