Variant report

Variant	rs560239
Chromosome Location	chr12:31771689-31771690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:31771681-31771874	K562	blood:	n/a	n/a
2	CEBPB	chr12:31771682-31771882	K562	blood:	n/a	n/a
3	JUND	chr12:31771202-31772076	K562	blood:	n/a	n/a
4	SPI1	chr12:31771606-31771851	GM12878	blood:	n/a	n/a
5	STAT1	chr12:31771261-31771855	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr12:31771177-31772047	K562	blood:	n/a	n/a
7	TEAD4	chr12:31771131-31772131	K562	blood:	n/a	n/a
8	SPI1	chr12:31771647-31771820	K562	blood:	n/a	n/a
9	EP300	chr12:31771214-31772018	K562	blood:	n/a	n/a
10	SPI1	chr12:31771643-31771934	GM12891	blood:	n/a	n/a
11	MYC	chr12:31771247-31771854	K562	blood:	n/a	n/a
12	ATF1	chr12:31771217-31771789	K562	blood:	n/a	n/a
13	STAT5A	chr12:31771407-31771856	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:31771672-31771722	GM19239	blood:	n/a
2	chr12:31771672-31771722	AG04450	lung:	fetal
3	chr12:31771672-31771722	SK-N-MC	brain:	n/a
4	chr12:31771672-31771722	CMK	blood:	n/a
5	chr12:31771672-31771722	K562	blood:	n/a
6	chr12:31771672-31771722	HEEpiC	esophagus:	n/a
7	chr12:31771672-31771722	NHDF-neo	bronchial:	n/a
8	chr12:31771672-31771722	SK-N-SH_RA	brain:	n/a
9	chr12:31771672-31771722	HCF	heart:	n/a
10	chr12:31771672-31771722	HIPEpiC	eye:	n/a
11	chr12:31771672-31771722	RPTEC	kidney:	n/a
12	chr12:31771672-31771722	PANC-1	pancreas:	n/a
13	chr12:31771672-31771722	T-47D	breast:	n/a
14	chr12:31771672-31771722	HL-60	blood:	n/a
15	chr12:31771672-31771722	BJ	skin:	n/a
16	chr12:31771672-31771722	LNCaP	prostate:	n/a
17	chr12:31771672-31771722	AoSMC	blood vessel:	n/a
18	chr12:31771672-31771722	PrEC	prostate:	n/a
19	chr12:31771672-31771722	NB4	blood:	n/a
20	chr12:31771672-31771722	MCF-7	breast:	n/a
21	chr12:31771672-31771722	U87	brain:	n/a
22	chr12:31771672-31771722	AG09309	skin:	n/a
23	chr12:31771672-31771722	SAEC	small airway:	n/a
24	chr12:31771672-31771722	HRPEpiC	eye:	n/a
25	chr12:31771672-31771722	HNPCEpiC	eye:	n/a
26	chr12:31771672-31771722	AG04449	skin:	fetal
27	chr12:31771672-31771722	NH-A	brain:	n/a
28	chr12:31771672-31771722	H1-hESC	embryonic stem cell:	embryo
29	chr12:31771672-31771722	HEK293	kidney:	embryo
30	chr12:31771672-31771722	HUVEC	blood vessel:	n/a
31	chr12:31771672-31771722	ProgFib	skin:	n/a
32	chr12:31771672-31771722	HCM	heart:	n/a
33	chr12:31771672-31771722	GM12891	blood:	n/a
34	chr12:31771672-31771722	HCT-116	colon:	n/a
35	chr12:31771672-31771722	HRCEpiC	kidney:	n/a
36	chr12:31771672-31771722	HPAEpiC	pulmonary alveolar:	n/a
37	chr12:31771672-31771722	AG10803	skin:	n/a
38	chr12:31771672-31771722	SK-N-SH	brain:	n/a
39	chr12:31771672-31771722	BE2_C	brain:	n/a
40	chr12:31771672-31771722	A549	lung:	n/a
41	chr12:31771672-31771722	NHBE	bronchial:	n/a
42	chr12:31771672-31771722	HAEpiC	amniotic membrane:	n/a
43	chr12:31771672-31771722	GM12892	blood:	n/a
44	chr12:31771672-31771722	HRE	kidney:	n/a
45	chr12:31771672-31771722	GM06990	blood:	n/a
46	chr12:31771672-31771722	Caco-2	colon:	n/a
47	chr12:31771672-31771722	ECC-1	luminal epithelium:	n/a
48	chr12:31771672-31771722	IMR90	lung:	fetal
49	chr12:31771672-31771722	HepG2	liver:	n/a
50	chr12:31771672-31771722	AG09319	gingival:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31770731..31773142-chr12:31773203..31775587,2	K562	blood:

No data

Variant related genes	Relation type
AK4P3	TF binding region
AK4P3	CpG island

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10843975	0.84[JPT][hapmap]
rs11051486	0.82[CEU][hapmap];1.00[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051497	0.85[ASN][1000 genomes]
rs12305966	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1677172	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716207	0.90[ASN][1000 genomes]
rs2374170	0.84[JPT][hapmap]
rs2447707	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2625881	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625882	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625884	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474909	0.85[ASN][1000 genomes]
rs476864	0.90[ASN][1000 genomes]
rs477758	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478620	0.89[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs509500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529303	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538400	0.92[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538430	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539102	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569482	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570329	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298559	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv983305	chr12:31767612-31773026	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31771000-31772600	Enhancers	GM12878-XiMat	blood
2	chr12:31771200-31772200	Enhancers	K562	blood
3	chr12:31771200-31774600	Enhancers	Fetal Intestine Large	intestine
4	chr12:31771400-31771800	Enhancers	Hela-S3	cervix
5	chr12:31771400-31772000	Enhancers	HSMMtube	muscle
6	chr12:31771400-31772000	Enhancers	NH-A	brain
7	chr12:31771400-31772600	Enhancers	Fetal Heart	heart
8	chr12:31771400-31772600	Enhancers	Small Intestine	intestine
9	chr12:31771400-31775400	Enhancers	Fetal Intestine Small	intestine
10	chr12:31771600-31771800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:31771600-31772000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:31771600-31772000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:31771600-31772000	Enhancers	A549	lung
14	chr12:31771600-31772200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:31771600-31772800	Enhancers	Ovary	ovary
16	chr12:31771600-31773600	Enhancers	HepG2	liver

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