Variant report

Variant	rs58729350
Chromosome Location	chr12:10515974-10515975
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	RUNX3	chr12:10515233-10518021	GM12878	blood:	n/a	n/a
2	TRIM28	chr12:10515893-10516383	K562	blood:	n/a	n/a
3	CBX3	chr12:10515912-10516253	K562	blood:	n/a	n/a
4	JUN	chr12:10515572-10516378	K562	blood:	n/a	n/a
5	EBF1	chr12:10515461-10516061	GM12878	blood:	n/a	chr12:10515760-10515771 chr12:10515721-10515732
6	TAL1	chr12:10515910-10516302	K562	blood:	n/a	n/a
7	RUNX3	chr12:10515310-10516011	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:10515864-10517381	K562	blood:	n/a	n/a
9	NR2F2	chr12:10515866-10516350	K562	blood:	n/a	n/a
10	MYC	chr12:10515722-10516276	K562	blood:	n/a	n/a
11	EBF1	chr12:10515436-10516292	GM12878	blood:	n/a	chr12:10515760-10515771 chr12:10515721-10515732
12	IRF1	chr12:10515959-10518392	K562	blood:	n/a	chr12:10517695-10517716
13	PML	chr12:10515927-10516338	K562	blood:	n/a	n/a
14	UBTF	chr12:10515864-10516222	K562	blood:	n/a	n/a
15	NFIC	chr12:10515243-10518076	GM12878	blood:	n/a	n/a
16	TCF7L2	chr12:10515599-10516587	HEK293	kidney:	n/a	n/a
17	FOXM1	chr12:10515269-10517964	GM12878	blood:	n/a	n/a
18	RELA	chr12:10515389-10515979	GM12878	blood:	n/a	n/a
19	CEBPD	chr12:10515852-10516373	K562	blood:	n/a	n/a
20	CEBPB	chr12:10515495-10517606	GM12878	blood:	n/a	n/a
21	GATA1	chr12:10515959-10516447	K562	blood:	n/a	n/a
22	STAT5A	chr12:10515777-10516351	K562	blood:	n/a	n/a
23	NR2F2	chr12:10515765-10516468	K562	blood:	n/a	n/a
24	REST	chr12:10515946-10516206	K562	blood:	n/a	n/a
25	TBP	chr12:10515796-10516422	K562	blood:	n/a	n/a
26	ATF2	chr12:10515391-10516378	GM12878	blood:	n/a	n/a
27	ZBTB7A	chr12:10515852-10516287	K562	blood:	n/a	n/a
28	RCOR1	chr12:10515717-10516714	K562	blood:	n/a	n/a
29	RELA	chr12:10515309-10516417	GM19099	blood:	n/a	n/a
30	POLR2A	chr12:10515946-10517794	K562	blood:	n/a	n/a
31	MTA3	chr12:10515355-10518224	GM12878	blood:	n/a	n/a
32	ATF3	chr12:10515933-10516347	K562	blood:	n/a	n/a
33	STAT5A	chr12:10515524-10515990	GM12878	blood:	n/a	n/a
34	CEBPB	chr12:10515912-10516396	K562	blood:	n/a	n/a
35	EBF1	chr12:10515549-10516047	GM12878	blood:	n/a	chr12:10515760-10515771 chr12:10515721-10515732
36	TEAD4	chr12:10515821-10516624	K562	blood:	n/a	n/a
37	TEAD4	chr12:10515861-10516377	K562	blood:	n/a	n/a
38	ATF2	chr12:10515378-10516482	GM12878	blood:	n/a	n/a
39	TBL1XR1	chr12:10515872-10516665	K562	blood:	n/a	n/a
40	POLR2A	chr12:10515888-10516346	K562	blood:	n/a	n/a
41	RELA	chr12:10515160-10518228	GM12891	blood:	n/a	n/a
42	JUND	chr12:10515840-10517315	K562	blood:	n/a	n/a
43	KAP1	chr12:10515697-10518370	U2OS	brain:	n/a	n/a
44	GATA2	chr12:10515888-10516373	K562	blood:	n/a	n/a
45	ARID3A	chr12:10515922-10516407	K562	blood:	n/a	n/a
46	STAT5A	chr12:10515947-10516370	K562	blood:	n/a	n/a
47	CEBPD	chr12:10515840-10516315	K562	blood:	n/a	n/a
48	JUN	chr12:10515928-10516384	K562	blood:	n/a	n/a
49	MTA3	chr12:10515501-10518202	GM12878	blood:	n/a	n/a
50	IRF1	chr12:10515759-10518375	K562	blood:	n/a	chr12:10517695-10517716

Variant related genes	Relation type
ENSG00000245648	TF binding region
ENSG00000256155	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs55670136	0.82[AMR][1000 genomes]
rs74060354	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3432683	chr12:10470734-10527581	Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3351751	chr12:10472734-10522269	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv898760	chr12:10492982-10564329	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv898761	chr12:10496724-10564329	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1036390	chr12:10496724-10596720	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv557455	chr12:10508975-10560957	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription 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	9 gene(s)	inside rSNPs	diseases
10	nsv898762	chr12:10509383-10564329	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv898763	chr12:10514528-10603670	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10511600-10516400	Weak transcription	Gastric	stomach
2	chr12:10511800-10516200	Weak transcription	Thymus	Thymus
3	chr12:10513000-10516400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr12:10513400-10516200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr12:10513400-10517000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:10513600-10516200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:10513600-10516400	Enhancers	Fetal Lung	lung
8	chr12:10513600-10516400	Enhancers	Osteobl	bone
9	chr12:10513600-10516600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:10513600-10516600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:10513600-10516600	Weak transcription	Aorta	Aorta
12	chr12:10514000-10516200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:10514000-10516200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:10514000-10516400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:10514000-10516400	Weak transcription	Pancreas	Pancrea
16	chr12:10514000-10516600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr12:10514000-10516800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:10514000-10517200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:10514200-10516800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:10514400-10516200	Enhancers	Fetal Intestine Large	intestine
21	chr12:10514400-10516400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:10514400-10516400	Enhancers	Brain Cingulate Gyrus	brain
23	chr12:10514400-10516400	Enhancers	Brain Substantia Nigra	brain
24	chr12:10514400-10516400	Enhancers	Placenta	Placenta
25	chr12:10514400-10516400	Enhancers	Stomach Mucosa	stomach
26	chr12:10514400-10516400	Weak transcription	HSMMtube	muscle
27	chr12:10514400-10516600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr12:10514600-10516000	Weak transcription	Brain Angular Gyrus	brain
29	chr12:10514600-10516400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr12:10514600-10516400	Enhancers	GM12878-XiMat	blood
31	chr12:10514600-10516600	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr12:10514600-10516600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr12:10514800-10516200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr12:10514800-10516200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:10514800-10516400	Weak transcription	A549	lung
36	chr12:10514800-10517000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr12:10515000-10516000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:10515000-10516200	Enhancers	HUVEC	blood vessel
39	chr12:10515000-10516400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:10515000-10516400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:10515000-10516400	Weak transcription	Left Ventricle	heart
42	chr12:10515000-10516600	Enhancers	Primary B cells from cord blood	blood
43	chr12:10515000-10516600	Enhancers	Primary T cells fromperipheralblood	blood
44	chr12:10515000-10516600	Enhancers	Fetal Thymus	thymus
45	chr12:10515000-10516800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:10515000-10516800	Enhancers	Dnd41	blood
47	chr12:10515000-10517200	Flanking Active TSS	NHEK	skin
48	chr12:10515200-10516000	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr12:10515200-10516400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:10515200-10516400	Enhancers	Primary T cells from cord blood	blood

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