Variant report

Variant	rs200548341
Chromosome Location	chr1:59247724-59247725
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:233)
CpG islands
(count:0)
Chromatin interactive
region (count:66)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:233 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:59247301-59248512	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:59244106-59251818	U87	brain:	n/a	n/a
3	POLR2A	chr1:59245147-59251676	Hela-S3	cervix:	n/a	n/a
4	SIN3AK20	chr1:59247212-59248438	MCF-7	breast:	n/a	n/a
5	MAX	chr1:59247473-59251323	GM12878	blood:	n/a	chr1:59249843-59249852
6	POLR2A	chr1:59247151-59251494	GM12892	blood:	n/a	n/a
7	SIN3AK20	chr1:59247248-59248101	SK-N-SH	brain:	n/a	n/a
8	PML	chr1:59247342-59247965	GM12878	blood:	n/a	n/a
9	USF2	chr1:59247379-59248269	GM12878	blood:	n/a	n/a
10	CTCF	chr1:59247339-59247740	K562	blood:	n/a	n/a
11	POLR2A	chr1:59247671-59250698	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:59243934-59251872	U87	brain:	n/a	n/a
13	GTF2F1	chr1:59247516-59247806	Hela-S3	cervix:	n/a	n/a
14	CHD1	chr1:59244118-59252745	IMR90	lung:	n/a	chr1:59250203-59250213
15	POLR2A	chr1:59247234-59250280	H1-hESC	embryonic stem cell:	n/a	n/a
16	HEY1	chr1:59246437-59251188	K562	blood:	n/a	chr1:59250260-59250275 chr1:59249195-59249210
17	POLR2A	chr1:59244614-59251725	HUVEC	blood vessel:	n/a	n/a
18	EP300	chr1:59247464-59247726	K562	blood:	n/a	n/a
19	FOXM1	chr1:59247385-59247988	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:59247171-59251601	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:59247385-59248444	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr1:59247074-59248139	HUVEC	blood vessel:	n/a	n/a
23	ZKSCAN1	chr1:59247347-59250548	Hela-S3	cervix:	n/a	n/a
24	MAX	chr1:59247373-59250292	H1-hESC	embryonic stem cell:	n/a	chr1:59249843-59249852
25	CHD2	chr1:59247295-59248282	Hela-S3	cervix:	n/a	n/a
26	CHD2	chr1:59247403-59248352	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:59247146-59251217	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:59247394-59248094	MCF-7	breast:	n/a	n/a
29	POLR2A	chr1:59244523-59251294	SK-N-SH	brain:	n/a	n/a
30	HEY1	chr1:59247490-59248096	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:59245241-59249887	K562	blood:	n/a	n/a
32	CTCF	chr1:59247382-59248359	K562	blood:	n/a	n/a
33	RFX5	chr1:59247427-59247786	Hela-S3	cervix:	n/a	n/a
34	SMC3	chr1:59247361-59247744	K562	blood:	n/a	n/a
35	POLR2A	chr1:59247451-59251336	GM12892	blood:	n/a	n/a
36	RAD21	chr1:59247406-59252535	IMR90	lung:	n/a	chr1:59249492-59249505 chr1:59250252-59250265 chr1:59249113-59249126
37	GTF2F1	chr1:59247354-59248461	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF7	chr1:59247674-59250323	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr1:59247048-59251502	GM12892	blood:	n/a	n/a
40	GATA3	chr1:59247268-59248516	A549	lung:	n/a	n/a
41	CTCF	chr1:59247450-59247733	H1-hESC	embryonic stem cell:	n/a	n/a
42	CCNT2	chr1:59247344-59251139	K562	blood:	n/a	chr1:59251021-59251030 chr1:59251014-59251023 chr1:59249183-59249192
43	BHLHE40	chr1:59247406-59250244	GM12878	blood:	n/a	chr1:59249401-59249417 chr1:59248756-59248769 chr1:59249198-59249214 chr1:59249193-59249209 chr1:59249190-59249206
44	CTCF	chr1:59247600-59247750	BE2_C	brain:	n/a	n/a
45	MXI1	chr1:59247319-59251329	HepG2	liver:	n/a	chr1:59249837-59249852
46	POLR2A	chr1:59247252-59251594	GM18526	blood:	n/a	n/a
47	POLR2A	chr1:59247177-59251727	Hela-S3	cervix:	n/a	n/a
48	RAD21	chr1:59247422-59248375	H1-hESC	embryonic stem cell:	n/a	n/a
49	SMC3	chr1:59247620-59247751	HepG2	liver:	n/a	n/a
50	CTCF	chr1:59247224-59251822	SK-N-SH	brain:	n/a	chr1:59250074-59250087 chr1:59249491-59249504 chr1:59248879-59248892 chr1:59249282-59249298 chr1:59250251-59250264 chr1:59249283-59249296 chr1:59248833-59248846

No data

(count:66 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr1:59246774..59249251-chr1:59451300..59453191,2	K562	blood:
2	chr1:59245914..59247946-chr1:59568208..59571099,2	K562	blood:
3	chr1:59245185..59249625-chr1:59318506..59322949,5	K562	blood:
4	chr1:59245650..59249709-chr1:60164316..60166597,3	MCF-7	breast:
5	chr1:59245489..59255081-chr1:59277954..59283925,49	MCF-7	breast:
6	chr1:59247150..59249652-chr1:59355694..59357549,2	MCF-7	breast:
7	chr1:59246163..59248652-chr1:59466870..59469148,2	K562	blood:
8	chr1:59247291..59249563-chr1:59804823..59806731,2	K562	blood:
9	chr1:59246529..59249235-chr1:59474703..59476422,2	K562	blood:
10	chr1:59247112..59247904-chr3:50336459..50337013,2	Hela-S3	cervix:
11	chr1:59245578..59252912-chr1:59759683..59766457,13	MCF-7	breast:
12	chr1:59246264..59248102-chr1:149855755..149857816,2	MCF-7	breast:
13	chr1:59244238..59248031-chr1:59689062..59692608,4	K562	blood:
14	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
15	chr1:59245136..59249509-chr1:59544104..59550391,6	K562	blood:
16	chr1:59246525..59249398-chr1:60121634..60124612,2	K562	blood:
17	chr1:59245974..59248964-chr1:60182800..60185774,2	MCF-7	breast:
18	chr1:59246648..59248452-chr1:59606800..59609133,2	K562	blood:
19	chr1:59246838..59249667-chr1:59504276..59507925,4	K562	blood:
20	chr1:59186058..59188120-chr1:59245328..59247867,2	K562	blood:
21	chr1:59245887..59249534-chr1:59455949..59458682,3	K562	blood:
22	chr1:59244053..59249750-chr1:59393075..59399809,12	K562	blood:
23	chr1:59247660..59249261-chr1:59326768..59328328,2	K562	blood:
24	chr1:59246435..59249254-chr1:59487144..59489692,2	MCF-7	breast:
25	chr1:59244169..59247928-chr1:60060481..60064138,5	K562	blood:
26	chr1:59203533..59207535-chr1:59246122..59248670,4	K562	blood:
27	chr1:59247110..59249752-chr1:59387312..59390458,3	K562	blood:
28	chr1:59245573..59247756-chr1:59431368..59433217,2	K562	blood:
29	chr1:59246122..59248225-chr1:60208395..60212049,3	K562	blood:
30	chr1:59245718..59248161-chr1:59323277..59324885,2	MCF-7	breast:
31	chr1:59163564..59170812-chr1:59245390..59251956,13	K562	blood:
32	chr1:59245933..59248490-chr1:59559542..59562151,2	K562	blood:
33	chr1:59246671..59249127-chr1:59295559..59298699,3	K562	blood:
34	chr1:59245570..59248484-chr1:61782798..61784305,2	K562	blood:
35	chr1:59244876..59251429-chr1:59540803..59548111,10	K562	blood:
36	chr1:59245275..59248106-chr1:59562308..59564391,2	K562	blood:
37	chr1:59247175..59249150-chr1:59885978..59888095,2	K562	blood:
38	chr1:59245909..59247878-chr1:59481525..59484880,3	K562	blood:
39	chr1:59243458..59255133-chr1:59272031..59283720,29	K562	blood:
40	chr1:59245308..59247839-chr1:60213241..60216132,2	K562	blood:
41	chr1:59176336..59177899-chr1:59247629..59249270,2	K562	blood:
42	chr1:59246945..59249154-chr1:59305966..59308006,2	K562	blood:
43	chr1:59229058..59237226-chr1:59244356..59250672,11	MCF-7	breast:
44	chr1:59245007..59249031-chr1:59898130..59900045,3	MCF-7	breast:
45	chr1:59162606..59168890-chr1:59243728..59252069,16	K562	blood:
46	chr1:59245349..59248652-chr1:59463306..59469148,5	K562	blood:
47	chr1:59010838..59012578-chr1:59247144..59249684,2	K562	blood:
48	chr1:59246576..59248497-chr1:59492481..59494688,2	K562	blood:
49	chr1:59243478..59247843-chr1:59300321..59305374,5	K562	blood:
50	chr1:59247050..59248597-chr1:59321085..59323549,2	K562	blood:

No data

Variant related genes	Relation type
LINC01135	TF binding region
ENSG00000228121	Chromatin interaction
ENSG00000162600	Chromatin interaction
ENSG00000235215	Chromatin interaction
ENSG00000222168	Chromatin interaction
ENSG00000243477	Chromatin interaction
ENSG00000264081	Chromatin interaction
ENSG00000232453	Chromatin interaction
ENSG00000186792	Chromatin interaction
ENSG00000173406	Chromatin interaction
ENSG00000172456	Chromatin interaction
ENSG00000272226	Chromatin interaction
ENSG00000162601	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798968	chr1:59246581-59251097	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1799803	chr1:59246581-59251097	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv12569	chr1:59247251-59250394	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	52 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	chr1:59245200-59251400	Active TSS	Aorta	Aorta
2	chr1:59245600-59250600	Active TSS	HMEC	breast
3	chr1:59245600-59251000	Active TSS	HSMMtube	muscle
4	chr1:59245600-59251400	Active TSS	Psoas Muscle	Psoas
5	chr1:59245800-59248400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:59245800-59248400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
7	chr1:59245800-59248800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
8	chr1:59246000-59247800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:59246000-59248000	Active TSS	Right Atrium	heart
10	chr1:59246000-59248400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:59246000-59251200	Active TSS	Liver	Liver
12	chr1:59246200-59248800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:59246200-59251600	Active TSS	Fetal Kidney	kidney
14	chr1:59246400-59248600	Transcr. at gene 5' and 3'	Osteobl	bone
15	chr1:59246400-59251400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:59246600-59247800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:59246600-59247800	Active TSS	Lung	lung
18	chr1:59246600-59248200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:59246600-59248400	Transcr. at gene 5' and 3'	Placenta Amnion	Placenta Amnion
20	chr1:59246600-59248400	Active TSS	GM12878-XiMat	blood
21	chr1:59246600-59249000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
22	chr1:59246600-59251200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:59246600-59251200	Active TSS	A549	lung
24	chr1:59246600-59251400	Active TSS	Ovary	ovary
25	chr1:59246800-59248800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:59246800-59248800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
27	chr1:59246800-59249400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
28	chr1:59246800-59249600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:59246800-59251000	Active TSS	HSMM	muscle
30	chr1:59246800-59251200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:59246800-59251400	Active TSS	Colon Smooth Muscle	Colon
32	chr1:59246800-59252000	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:59247000-59247800	Active TSS	Brain Cingulate Gyrus	brain
34	chr1:59247000-59247800	Flanking Active TSS	Hela-S3	cervix
35	chr1:59247000-59248200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:59247000-59248400	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr1:59247000-59248800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr1:59247000-59248800	Transcr. at gene 5' and 3'	NHEK	skin
39	chr1:59247000-59249000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr1:59247000-59249000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr1:59247000-59249000	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr1:59247000-59249200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:59247000-59249400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr1:59247000-59251200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:59247000-59251200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:59247000-59251200	Active TSS	Brain Angular Gyrus	brain
47	chr1:59247000-59251200	Active TSS	Brain Anterior Caudate	brain
48	chr1:59247000-59251200	Active TSS	Brain Hippocampus Middle	brain
49	chr1:59247000-59251200	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr1:59247000-59251200	Active TSS	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links