Variant report

Variant	rs17688567
Chromosome Location	chr12:30906358-30906359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:185)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:185 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:30906320-30906470	GM06990	blood:	n/a	n/a
2	CTCF	chr12:30906260-30906410	HAc	cerebellar:	n/a	n/a
3	YY1	chr12:30906284-30906491	K562	blood:	n/a	n/a
4	CTCF	chr12:30906280-30906430	BE2_C	brain:	n/a	n/a
5	POLR2A	chr12:30906113-30906454	MCF10A-Er-Src	breast:	n/a	n/a
6	SMC3	chr12:30906139-30906603	HepG2	liver:	n/a	n/a
7	RAD21	chr12:30906270-30906509	SK-N-SH_RA	brain:	n/a	n/a
8	UBTF	chr12:30906300-30906638	K562	blood:	n/a	n/a
9	CTCF	chr12:30906260-30906410	GM12878	blood:	n/a	n/a
10	CTCF	chr12:30906357-30906449	MCF-7	breast:	n/a	n/a
11	POLR2A	chr12:30906266-30906599	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr12:30906340-30906490	HCT-116	colon:	n/a	n/a
13	CTCF	chr12:30906277-30906561	K562	blood:	n/a	n/a
14	MXI1	chr12:30906275-30908913	IMR90	lung:	n/a	n/a
15	CTCF	chr12:30906320-30906470	A549	lung:	n/a	n/a
16	CTCF	chr12:30906193-30906547	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr12:30906248-30906479	HUVEC	blood vessel:	n/a	n/a
18	CTCF	chr12:30906320-30906470	HPF	lung:	n/a	n/a
19	CTCF	chr12:30906286-30906503	K562	blood:	n/a	n/a
20	SMC3	chr12:30906246-30906532	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr12:30906320-30906470	WERI-Rb-1	eye:	n/a	n/a
22	CTCF	chr12:30906280-30906430	GM12874	blood:	n/a	n/a
23	MYC	chr12:30906154-30906618	K562	blood:	n/a	n/a
24	CTCF	chr12:30906320-30906470	HMF	breast:	n/a	n/a
25	ARID3A	chr12:30906154-30906474	K562	blood:	n/a	n/a
26	CTCF	chr12:30906220-30906370	GM12870	blood:	n/a	n/a
27	CTCF	chr12:30906260-30906410	GM12875	blood:	n/a	n/a
28	RAD21	chr12:30906282-30906521	K562	blood:	n/a	n/a
29	CTCF	chr12:30906296-30906471	SK-N-SH_RA	brain:	n/a	n/a
30	CTCF	chr12:30906280-30906430	GM12873	blood:	n/a	n/a
31	CTCF	chr12:30906340-30906490	HRPEpiC	eye:	n/a	n/a
32	CTCF	chr12:30906218-30906563	GM12878	blood:	n/a	n/a
33	CTCF	chr12:30906280-30906430	HCPEpiC	choroid plexus:	n/a	n/a
34	TBL1XR1	chr12:30906209-30906467	K562	blood:	n/a	n/a
35	CTCF	chr12:30906300-30906450	HCM	heart:	n/a	n/a
36	CTCF	chr12:30906240-30906390	GM12864	blood:	n/a	n/a
37	RAD21	chr12:30906257-30906559	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr12:30906280-30906430	GM12868	blood:	n/a	n/a
39	CTCF	chr12:30906320-30906470	GM12864	blood:	n/a	n/a
40	CTCF	chr12:30905966-30908651	A549	lung:	n/a	chr12:30907136-30907144
41	CTCF	chr12:30906300-30906450	K562	blood:	n/a	n/a
42	MAX	chr12:30906255-30906563	NB4	blood:	n/a	n/a
43	CTCF	chr12:30906008-30907595	SK-N-SH	brain:	n/a	chr12:30907136-30907144
44	RAD21	chr12:30906206-30906616	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr12:30906283-30906524	Hela-S3	cervix:	n/a	n/a
46	CEBPB	chr12:30906315-30906675	K562	blood:	n/a	n/a
47	RCOR1	chr12:30906335-30906712	HepG2	liver:	n/a	n/a
48	ZNF143	chr12:30906342-30906536	GM12878	blood:	n/a	n/a
49	CTCF	chr12:30906300-30906450	HEK293	kidney:	n/a	n/a
50	CTCF	chr12:30906320-30906470	SK-N-SH_RA	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30906304..30909589-chr12:30948532..30951386,3	K562	blood:
2	chr12:30902650..30905580-chr12:30906095..30908998,3	MCF-7	breast:

No data

Variant related genes	Relation type
CAPRIN2	TF binding region
ENSG00000246331	TF binding region
ENSG00000110888	Chromatin interaction
ENSG00000235884	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11608803	0.96[AMR][1000 genomes]
rs11613738	0.89[AMR][1000 genomes]
rs17486840	0.89[AMR][1000 genomes]
rs17560141	0.96[AMR][1000 genomes]
rs17687472	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17687791	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17687846	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17687964	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17739338	0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2099029	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2882856	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4459394	0.89[AMR][1000 genomes]
rs4930937	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4931357	0.89[AMR][1000 genomes]
rs4931358	0.96[AMR][1000 genomes]
rs4931359	0.93[AMR][1000 genomes]
rs4931363	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55957969	0.96[AMR][1000 genomes]
rs73077865	0.81[AMR][1000 genomes]
rs73077869	0.96[AMR][1000 genomes]
rs73077870	0.96[AMR][1000 genomes]
rs73077877	0.96[AMR][1000 genomes]
rs73077884	0.96[AMR][1000 genomes]
rs73077887	0.96[AMR][1000 genomes]
rs73077893	0.96[AMR][1000 genomes]
rs73079959	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73079962	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73079965	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73079966	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73079970	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73079971	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73079996	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30861400-30906600	Weak transcription	Small Intestine	intestine
2	chr12:30863400-30906400	Weak transcription	Spleen	Spleen
3	chr12:30863400-30906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:30876000-30906600	Weak transcription	Fetal Intestine Small	intestine
5	chr12:30878800-30906600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:30882000-30906800	Weak transcription	Psoas Muscle	Psoas
7	chr12:30882200-30906400	Weak transcription	Lung	lung
8	chr12:30882200-30906400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:30882200-30906600	Weak transcription	Placenta	Placenta
10	chr12:30882200-30906800	Weak transcription	Esophagus	oesophagus
11	chr12:30882400-30906600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:30882600-30906400	Weak transcription	Right Ventricle	heart
13	chr12:30882800-30906800	Weak transcription	Gastric	stomach
14	chr12:30883200-30906400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr12:30886600-30906400	Weak transcription	Brain Substantia Nigra	brain
16	chr12:30888400-30906800	Weak transcription	Fetal Intestine Large	intestine
17	chr12:30892400-30906400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:30892400-30906400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:30892600-30906400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:30894800-30906400	Weak transcription	Stomach Mucosa	stomach
21	chr12:30897200-30906600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:30899600-30906600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:30900000-30906400	Weak transcription	Adipose Nuclei	Adipose
24	chr12:30900000-30906400	Weak transcription	Fetal Muscle Leg	muscle
25	chr12:30900000-30906600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:30900000-30906600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:30900000-30906800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:30900200-30906400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:30900400-30906400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:30900400-30906400	Weak transcription	Fetal Brain Male	brain
31	chr12:30900400-30906400	Weak transcription	Left Ventricle	heart
32	chr12:30900400-30906400	Weak transcription	Ovary	ovary
33	chr12:30900600-30906600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:30901000-30906600	Weak transcription	Liver	Liver
35	chr12:30901200-30906400	Weak transcription	Fetal Brain Female	brain
36	chr12:30902200-30906800	Weak transcription	Aorta	Aorta
37	chr12:30903000-30906400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:30903800-30908400	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr12:30904200-30906400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:30904600-30906400	Weak transcription	Pancreas	Pancrea
41	chr12:30904600-30906400	Weak transcription	Right Atrium	heart
42	chr12:30904800-30906400	Enhancers	Hela-S3	cervix
43	chr12:30905000-30906600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:30905200-30906400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:30905200-30906400	Enhancers	Brain Germinal Matrix	brain
46	chr12:30905200-30906400	Enhancers	GM12878-XiMat	blood
47	chr12:30905200-30906400	Enhancers	HUVEC	blood vessel
48	chr12:30905200-30906600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:30905200-30906600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr12:30905200-30906600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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