Variant report

Variant	rs7294729
Chromosome Location	chr12:9515959-9515960
allele	C/T
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	BATF	chr12:9515676-9516129	GM12878	blood:	n/a	chr12:9515939-9515950
2	POLR2A	chr12:9515627-9516169	GM12891	blood:	n/a	n/a
3	TCF12	chr12:9515787-9516134	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr12:9515537-9518036	GM12878	blood:	n/a	n/a
5	MAZ	chr12:9515828-9516069	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:9515357-9518289	GM12891	blood:	n/a	n/a
7	MTA3	chr12:9513806-9518741	GM12878	blood:	n/a	n/a
8	YY1	chr12:9515789-9516040	K562	blood:	n/a	n/a
9	POLR2A	chr12:9515210-9518678	GM12892	blood:	n/a	n/a
10	RUNX3	chr12:9515617-9516177	GM12878	blood:	n/a	n/a
11	RCOR1	chr12:9515832-9516089	GM12878	blood:	n/a	n/a
12	JUND	chr12:9515780-9516074	HepG2	liver:	n/a	chr12:9515937-9515948
13	EBF1	chr12:9515717-9516051	GM12878	blood:	n/a	n/a
14	CHD2	chr12:9515653-9516070	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:9515459-9518442	GM12891	blood:	n/a	n/a
16	POLR2A	chr12:9515604-9516116	GM12878	blood:	n/a	n/a
17	ATF2	chr12:9514144-9518351	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:9515268-9518663	GM12892	blood:	n/a	n/a
19	POLR2A	chr12:9515784-9516132	GM12878	blood:	n/a	n/a
20	FOSL2	chr12:9515730-9516135	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:9515855-9518400	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:9515649-9516184	GM12891	blood:	n/a	n/a
23	POLR2A	chr12:9515686-9518336	GM12892	blood:	n/a	n/a
24	PML	chr12:9515398-9518380	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:9515277-9516245	GM12891	blood:	n/a	n/a
26	POLR2A	chr12:9515669-9518302	GM12878	blood:	n/a	n/a
27	USF2	chr12:9515851-9516035	GM12878	blood:	n/a	n/a
28	FOXM1	chr12:9515281-9516143	GM12878	blood:	n/a	n/a
29	ATF1	chr12:9515879-9516104	K562	blood:	n/a	n/a
30	RCOR1	chr12:9515770-9516044	K562	blood:	n/a	n/a
31	MTA3	chr12:9515491-9518616	GM12878	blood:	n/a	n/a
32	TCF12	chr12:9515828-9516145	GM12878	blood:	n/a	n/a
33	CTCF	chr12:9515880-9516030	GM12865	blood:	n/a	n/a
34	JUND	chr12:9515748-9516087	K562	blood:	n/a	chr12:9515937-9515948
35	ATF2	chr12:9515316-9516084	GM12878	blood:	n/a	n/a
36	RUNX3	chr12:9514192-9516260	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:9515282-9518433	GM12878	blood:	n/a	n/a
38	STAT5A	chr12:9515551-9518334	GM12878	blood:	n/a	chr12:9516641-9516655 chr12:9516596-9516607
39	POLR2A	chr12:9515243-9518471	GM12892	blood:	n/a	n/a
40	MAX	chr12:9515833-9516033	GM12878	blood:	n/a	n/a
41	POLR2A	chr12:9515223-9518659	GM12878	blood:	n/a	n/a
42	NFIC	chr12:9513911-9516290	GM12878	blood:	n/a	n/a
43	WRNIP1	chr12:9515543-9516016	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9514472..9517285-chr12:9517571..9520331,3	K562	blood:
2	chr12:9514676..9517481-chr12:9908794..9910668,2	K562	blood:

Variant related genes	Relation type
ENSG00000260423	TF binding region
ENSG00000260423	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10771596	0.94[YRI][hapmap]
rs10843520	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4883246	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4883247	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4883250	0.88[YRI][hapmap]
rs7298303	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs7313591	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7314241	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs741621	0.89[YRI][hapmap]
rs7956178	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1035958	chr12:9472365-9579109	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active 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	11 gene(s)	inside rSNPs	diseases
15	nsv898742	chr12:9473157-9518222	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv898743	chr12:9473157-9522350	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv975403	chr12:9481646-9541991	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	esv3436788	chr12:9499151-9519686	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv3332298	chr12:9500121-9519487	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv2760260	chr12:9504060-9519172	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9506800-9516000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:9507000-9516800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:9507000-9517200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:9512400-9516200	Strong transcription	Fetal Lung	lung
5	chr12:9514800-9517200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr12:9515000-9516000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:9515000-9517000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:9515000-9517800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:9515200-9516600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:9515400-9516800	Enhancers	HepG2	liver
11	chr12:9515400-9517000	Enhancers	HMEC	breast
12	chr12:9515400-9517200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:9515400-9519200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:9515600-9516000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:9515600-9516200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:9515600-9516200	Enhancers	NHEK	skin
17	chr12:9515600-9516800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:9515600-9517000	Flanking Active TSS	GM12878-XiMat	blood
19	chr12:9515600-9518600	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:9515800-9516000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:9515800-9516000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:9515800-9516000	Enhancers	Right Atrium	heart
23	chr12:9515800-9516800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:9515800-9517000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:9515800-9517200	Enhancers	K562	blood
26	chr12:9515800-9518200	Enhancers	HSMMtube	muscle
27	chr12:9515800-9518600	Enhancers	H9 Cell Line	embryonic stem cell
28	chr12:9515800-9520000	Enhancers	H1 Cell Line	embryonic stem cell
29	chr12:9515800-9520000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links