Variant report

Variant	rs12728679
Chromosome Location	chr1:114522285-114522286
allele	A/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	CTCF	chr1:114521139-114522552	A549	lung:	n/a	chr1:114521558-114521576 chr1:114521559-114521575 chr1:114521560-114521581 chr1:114521561-114521574
2	CTCF	chr1:114522140-114522290	K562	blood:	n/a	n/a
3	RAD21	chr1:114521930-114522347	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr1:114522140-114522290	HVMF	connective:	n/a	n/a
5	CTCF	chr1:114522140-114522290	NB4	blood:	n/a	n/a
6	POLR2A	chr1:114521735-114522434	U87	brain:	n/a	n/a
7	CTCF	chr1:114522140-114522290	RPTEC	kidney:	n/a	n/a
8	CTCF	chr1:114522140-114522290	HCT-116	colon:	n/a	n/a
9	MAX	chr1:114521890-114522367	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr1:114522220-114522370	GM12869	blood:	n/a	n/a
11	CTCF	chr1:114521181-114523331	MCF-7	breast:	n/a	chr1:114521558-114521576 chr1:114521559-114521575 chr1:114521560-114521581 chr1:114521561-114521574
12	CTCF	chr1:114521107-114522563	SK-N-SH	brain:	n/a	chr1:114521558-114521576 chr1:114521559-114521575 chr1:114521560-114521581 chr1:114521561-114521574
13	YY1	chr1:114521479-114522479	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr1:114522160-114522310	HepG2	liver:	n/a	n/a
15	GATA3	chr1:114521621-114522360	SK-N-SH	brain:	n/a	chr1:114521798-114521809
16	RAD21	chr1:114521258-114522427	HCT-116	colon:	n/a	chr1:114521559-114521578
17	SP1	chr1:114521735-114522331	H1-hESC	embryonic stem cell:	n/a	chr1:114521969-114521978 chr1:114522051-114522063 chr1:114522040-114522052 chr1:114521969-114521979 chr1:114521968-114521980 chr1:114522041-114522055 chr1:114522052-114522061 chr1:114522040-114522051 chr1:114522040-114522052 chr1:114522052-114522066 chr1:114522051-114522062 chr1:114521965-114521979 chr1:114522053-114522062 chr1:114522052-114522062
18	CTCF	chr1:114522160-114522310	AG04450	lung:	n/a	n/a
19	CTCF	chr1:114522160-114522310	HCT-116	colon:	n/a	n/a
20	RAD21	chr1:114521326-114522344	SK-N-SH_RA	brain:	n/a	chr1:114521559-114521578
21	CTCF	chr1:114522200-114522350	GM12864	blood:	n/a	n/a
22	JUND	chr1:114521419-114522364	H1-hESC	embryonic stem cell:	n/a	chr1:114521573-114521582
23	CTCF	chr1:114521982-114522414	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr1:114522057-114522381	GM12878	blood:	n/a	n/a
25	TBL1XR1	chr1:114522160-114522338	K562	blood:	n/a	n/a
26	SMC3	chr1:114521387-114522387	K562	blood:	n/a	chr1:114521560-114521574
27	CTCF	chr1:114522140-114522290	GM12865	blood:	n/a	n/a
28	CTCF	chr1:114522160-114522310	BE2_C	brain:	n/a	n/a
29	SMC3	chr1:114522106-114522341	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr1:114522200-114522350	GM12872	blood:	n/a	n/a
31	MAZ	chr1:114521316-114523213	IMR90	lung:	n/a	n/a
32	CTCF	chr1:114522113-114522308	A549	lung:	n/a	n/a
33	GTF2F1	chr1:114522046-114522301	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUN	chr1:114521826-114522457	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr1:114522135-114522291	MCF-7	breast:	n/a	n/a
36	CTCF	chr1:114522118-114522291	HUVEC	blood vessel:	n/a	n/a
37	RAD21	chr1:114522035-114522365	HepG2	liver:	n/a	n/a
38	CTCF	chr1:114522220-114522370	GM12867	blood:	n/a	n/a
39	RXRA	chr1:114521595-114522351	SK-N-SH	brain:	n/a	chr1:114522265-114522274 chr1:114521988-114521997
40	GATA3	chr1:114521523-114522306	SK-N-SH	brain:	n/a	chr1:114521798-114521809
41	SIN3A	chr1:114521412-114522324	H1-hESC	embryonic stem cell:	n/a	n/a
42	TEAD4	chr1:114521806-114522358	H1-hESC	embryonic stem cell:	n/a	n/a
43	EP300	chr1:114521428-114522439	SK-N-SH	brain:	n/a	chr1:114521983-114521997
44	EP300	chr1:114521575-114522323	SK-N-SH	brain:	n/a	chr1:114521983-114521997
45	MAX	chr1:114521898-114522321	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr1:114521286-114522425	HepG2	liver:	n/a	chr1:114521559-114521578
47	CTCF	chr1:114522160-114522310	BJ	skin:	n/a	n/a
48	CTCF	chr1:114522140-114522290	GM12869	blood:	n/a	n/a
49	POLR2A	chr1:114521748-114522359	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr1:114521773-114522295	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:114520876..114522533-chr16:67188885..67190007,9	MCF-7	breast:
2	chr1:114471506..114473104-chr1:114522240..114523784,2	K562	blood:
3	chr1:114520287..114523233-chr1:115052633..115055496,3	MCF-7	breast:

Variant related genes	Relation type
OLFML3	TF binding region
ENSG00000235527	Chromatin interaction
ENSG00000102871	Chromatin interaction
ENSG00000197323	Chromatin interaction
ENSG00000163349	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs17466149	1.00[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114516200-114524600	Weak transcription	Small Intestine	intestine
2	chr1:114517400-114522400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:114517400-114522400	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:114517600-114523400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:114518000-114524800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:114518200-114522600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:114518400-114523000	Weak transcription	Thymus	Thymus
8	chr1:114518400-114525600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:114518600-114525200	Weak transcription	Dnd41	blood
10	chr1:114518800-114525200	Weak transcription	GM12878-XiMat	blood
11	chr1:114518800-114525800	Weak transcription	Esophagus	oesophagus
12	chr1:114519000-114525000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:114519800-114527000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:114520000-114522400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:114521000-114522400	Enhancers	Fetal Heart	heart
16	chr1:114521000-114523200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:114521200-114522600	Weak transcription	Primary T cells from cord blood	blood
18	chr1:114521400-114523200	Flanking Active TSS	Osteobl	bone
19	chr1:114521600-114522400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:114521600-114522400	Flanking Active TSS	Fetal Intestine Small	intestine
21	chr1:114521600-114522400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr1:114521600-114522400	Enhancers	HMEC	breast
23	chr1:114521600-114522600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:114521600-114522600	Enhancers	Brain Substantia Nigra	brain
25	chr1:114521600-114522800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr1:114521600-114522800	Flanking Active TSS	Fetal Lung	lung
27	chr1:114521600-114523000	Active TSS	Duodenum Mucosa	Duodenum
28	chr1:114521600-114523000	Enhancers	Spleen	Spleen
29	chr1:114521600-114523000	Flanking Active TSS	NH-A	brain
30	chr1:114521600-114523200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr1:114521600-114523200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr1:114521600-114523200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:114521600-114523200	Active TSS	Colonic Mucosa	Colon
34	chr1:114521600-114523200	Active TSS	Right Atrium	heart
35	chr1:114521600-114523200	Flanking Active TSS	HSMMtube	muscle
36	chr1:114521600-114523400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr1:114521600-114523400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr1:114521600-114523600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:114521600-114523800	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr1:114521600-114524000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr1:114521600-114524200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:114521600-114526600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr1:114521600-114527000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:114521800-114522400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:114521800-114522400	Enhancers	Brain Germinal Matrix	brain
46	chr1:114521800-114522400	Flanking Active TSS	Fetal Brain Male	brain
47	chr1:114521800-114522400	Enhancers	Lung	lung
48	chr1:114521800-114522400	Active TSS	NHDF-Ad	bronchial
49	chr1:114521800-114522600	Active TSS	NHLF	lung
50	chr1:114521800-114522800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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