Variant report

Variant	rs762623
Chromosome Location	chr6:36645466-36645467
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	STAT3	chr6:36645054-36646335	MCF10A-Er-Src	breast:	n/a	chr6:36645802-36645822 chr6:36645808-36645817 chr6:36645808-36645816 chr6:36645802-36645822 chr6:36645807-36645816
2	RUNX3	chr6:36644763-36645901	GM12878	blood:	n/a	n/a
3	KAP1	chr6:36644788-36646792	HEK293	kidney:	n/a	n/a
4	NFIC	chr6:36645088-36646823	HepG2	liver:	n/a	n/a
5	ZNF143	chr6:36645448-36645673	GM12878	blood:	n/a	n/a
6	FOXA1	chr6:36645399-36646046	HepG2	liver:	n/a	n/a
7	ELF1	chr6:36645458-36645987	HepG2	liver:	n/a	chr6:36645809-36645818
8	MAZ	chr6:36645377-36649066	IMR90	lung:	n/a	chr6:36648002-36648011
9	TBP	chr6:36645416-36645915	HepG2	liver:	n/a	n/a
10	WRNIP1	chr6:36645250-36647385	GM12878	blood:	n/a	n/a
11	EP300	chr6:36645336-36646668	HepG2	liver:	n/a	n/a
12	HEY1	chr6:36644699-36647538	HepG2	liver:	n/a	chr6:36646439-36646454 chr6:36646399-36646414
13	RAD21	chr6:36643874-36649108	SK-N-SH	brain:	n/a	chr6:36644187-36644201 chr6:36646425-36646439 chr6:36646938-36646951 chr6:36647756-36647766 chr6:36644031-36644045
14	ZEB1	chr6:36644713-36647578	HepG2	liver:	n/a	n/a
15	CTCF	chr6:36644682-36649046	SK-N-SH	brain:	n/a	chr6:36644843-36644861 chr6:36647784-36647797 chr6:36646423-36646441 chr6:36645963-36645970 chr6:36647827-36647836 chr6:36647770-36647780
16	MXI1	chr6:36643959-36649033	IMR90	lung:	n/a	n/a
17	POLR2A	chr6:36643939-36647410	HepG2	liver:	n/a	n/a
18	POLR2A	chr6:36644766-36648199	MCF10A-Er-Src	breast:	n/a	n/a
19	TEAD4	chr6:36645211-36646668	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:36644776-36645864	GM19193	blood:	n/a	n/a
21	PML	chr6:36644718-36649008	GM12878	blood:	n/a	chr6:36648003-36648012
22	POLR2A	chr6:36644702-36645953	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:36645352-36648955	HepG2	liver:	n/a	n/a
24	POLR2A	chr6:36645411-36645734	GM12891	blood:	n/a	n/a
25	MAX	chr6:36643823-36648608	HepG2	liver:	n/a	chr6:36648002-36648011
26	POLR2A	chr6:36644830-36649007	GM12878	blood:	n/a	n/a
27	RELA	chr6:36645060-36646770	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:36644736-36646047	HepG2	liver:	n/a	n/a
29	MXI1	chr6:36643752-36648956	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr6:36645402-36645962	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:36644081-36649028	IMR90	lung:	n/a	n/a
32	POLR2A	chr6:36644870-36645864	HepG2	liver:	n/a	n/a
33	MYBL2	chr6:36644928-36647408	HepG2	liver:	n/a	n/a
34	SRF	chr6:36645457-36645973	HepG2	liver:	n/a	chr6:36645773-36645791 chr6:36645774-36645791
35	FOXA1	chr6:36645422-36646090	HepG2	liver:	n/a	n/a
36	NFIC	chr6:36645074-36647075	GM12878	blood:	n/a	n/a
37	MAZ	chr6:36645370-36645930	GM12878	blood:	n/a	n/a
38	ELK1	chr6:36645433-36645938	GM12878	blood:	n/a	n/a
39	RUNX3	chr6:36645420-36647630	GM12878	blood:	n/a	n/a
40	FOXA1	chr6:36645456-36646754	HepG2	liver:	n/a	n/a
41	ELF1	chr6:36645415-36645970	HepG2	liver:	n/a	chr6:36645809-36645818
42	NFIC	chr6:36644925-36646697	HepG2	liver:	n/a	n/a
43	MYBL2	chr6:36643933-36646660	HepG2	liver:	n/a	n/a
44	FOXA1	chr6:36645399-36646079	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:36643627-36647609	HepG2	liver:	n/a	n/a
46	POLR2A	chr6:36645391-36649020	GM12892	blood:	n/a	n/a
47	EP300	chr6:36645416-36646043	HepG2	liver:	n/a	n/a
48	POLR2A	chr6:36643787-36657761	GM12891	blood:	n/a	n/a
49	IKZF1	chr6:36644976-36646231	GM12878	blood:	n/a	chr6:36645950-36645958
50	KAP1	chr6:36644053-36645893	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36645391..36647920-chr6:36680659..36684331,3	MCF-7	breast:
2	chr17:57914670..57916833-chr6:36645394..36647964,3	MCF-7	breast:
3	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
4	chr6:36644040..36648031-chr6:36680924..36685784,5	MCF-7	breast:
5	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
6	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
7	chr6:36606453..36608701-chr6:36645452..36648033,2	MCF-7	breast:
8	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
9	chr6:36560169..36564521-chr6:36645252..36648947,8	MCF-7	breast:
10	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

Variant related genes	Relation type
CDKN1A	TF binding region
ENSG00000112081	Chromatin interaction
ENSG00000238554	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000263894	Chromatin interaction
ENSG00000255587	Chromatin interaction
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1321312	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1969701	0.93[ASN][1000 genomes]
rs1977172	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3176330	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3176331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3829966	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3829967	1.00[ASN][1000 genomes]
rs3829968	0.97[ASN][1000 genomes]
rs4135234	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4135237	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4135239	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713997	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4714000	0.89[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.97[ASN][1000 genomes]
rs6457936	0.97[ASN][1000 genomes]
rs6902994	0.84[ASN][1000 genomes]
rs6907801	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6926780	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7452626	0.89[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs9380585	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9380586	0.89[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][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	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs762623	CDKN1A	cis	multi-tissue	Pritchard

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
2	chr6:36640400-36645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:36642400-36646400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:36643600-36646000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:36643800-36645600	Enhancers	Adipose Nuclei	Adipose
6	chr6:36643800-36645600	Enhancers	Brain Angular Gyrus	brain
7	chr6:36643800-36645600	Enhancers	Fetal Intestine Large	intestine
8	chr6:36643800-36645600	Enhancers	Fetal Intestine Small	intestine
9	chr6:36643800-36645600	Enhancers	A549	lung
10	chr6:36643800-36645600	Enhancers	NHLF	lung
11	chr6:36643800-36645600	Enhancers	Osteobl	bone
12	chr6:36643800-36645800	Enhancers	HUVEC	blood vessel
13	chr6:36643800-36646000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:36643800-36646000	Enhancers	Brain Substantia Nigra	brain
15	chr6:36643800-36646000	Enhancers	NH-A	brain
16	chr6:36643800-36646200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:36643800-36646200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:36643800-36646400	Bivalent Enhancer	Fetal Thymus	thymus
19	chr6:36643800-36646400	Enhancers	Pancreas	Pancrea
20	chr6:36643800-36646400	Enhancers	Stomach Mucosa	stomach
21	chr6:36643800-36646400	Flanking Active TSS	NHEK	skin
22	chr6:36644000-36645600	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:36644000-36645600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:36644000-36645600	Enhancers	Hela-S3	cervix
25	chr6:36644000-36646000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:36644000-36646000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:36644000-36646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:36644000-36646000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:36644000-36646000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:36644000-36646000	Enhancers	Brain Anterior Caudate	brain
31	chr6:36644000-36646000	Enhancers	Colonic Mucosa	Colon
32	chr6:36644000-36646000	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr6:36644000-36646200	Enhancers	Esophagus	oesophagus
34	chr6:36644000-36646200	Flanking Active TSS	HSMM	muscle
35	chr6:36644000-36646400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:36644000-36646400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:36644000-36646400	Enhancers	Placenta	Placenta
38	chr6:36644000-36646400	Enhancers	Lung	lung
39	chr6:36644000-36646400	Flanking Active TSS	HMEC	breast
40	chr6:36644200-36645600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:36644200-36645600	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr6:36644200-36646000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:36644200-36646200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:36644200-36647600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:36644400-36646000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
46	chr6:36644400-36646000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr6:36644400-36646400	Weak transcription	Spleen	Spleen
48	chr6:36644600-36645800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
49	chr6:36644600-36645800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
50	chr6:36644600-36646000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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