Variant report

Variant	rs12227855
Chromosome Location	chr12:117316970-117316971
allele	A/C
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	CTBP2	chr12:117316706-117317573	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:117316325-117317095	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:117316331-117317010	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr12:117316311-117316987	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:117316446-117317053	Hela-S3	cervix:	n/a	n/a
6	ELK1	chr12:117316910-117317108	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:117316664-117317547	H1-neurons	neurons:	n/a	n/a
8	RFX5	chr12:117316340-117317081	Hela-S3	cervix:	n/a	n/a
9	SMARCB1	chr12:117316356-117318213	Hela-S3	cervix:	n/a	n/a
10	MAX	chr12:117316376-117317060	Hela-S3	cervix:	n/a	chr12:117316655-117316665
11	POLR2A	chr12:117316686-117317062	Hela-S3	cervix:	n/a	n/a
12	SUZ12	chr12:117316189-117319614	NT2-D1	testis:	n/a	n/a
13	GTF2F1	chr12:117316422-117317155	Hela-S3	cervix:	n/a	n/a
14	ZNF263	chr12:117316348-117317103	HEK293-T-REx	kidney:	n/a	chr12:117316779-117316788
15	ZKSCAN1	chr12:117316547-117317086	Hela-S3	cervix:	n/a	n/a
16	MXI1	chr12:117316397-117317020	Hela-S3	cervix:	n/a	n/a
17	MAZ	chr12:117316310-117317076	Hela-S3	cervix:	n/a	chr12:117316655-117316665
18	POLR2A	chr12:117316645-117316973	MCF10A-Er-Src	breast:	n/a	n/a
19	RCOR1	chr12:117316288-117317050	Hela-S3	cervix:	n/a	n/a
20	TFAP2A	chr12:117316254-117317069	Hela-S3	cervix:	n/a	chr12:117316448-117316463
21	TFAP2C	chr12:117316201-117317098	Hela-S3	cervix:	n/a	n/a
22	HDAC2	chr12:117316283-117317121	MCF-7	breast:	n/a	chr12:117317061-117317075
23	POLR2A	chr12:117316313-117317030	HCT-116	colon:	n/a	n/a
24	POLR2A	chr12:117316234-117317093	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117174783..117176988-chr12:117316113..117318785,2	MCF-7	breast:
2	chr12:117314859..117317028-chr12:117347500..117350151,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HRK-1	chr12:117316878-117317422	NONHSAT030971

Variant related genes	Relation type
HRK	TF binding region
ENSG00000135119	Chromatin interaction
ENSG00000111412	Chromatin interaction
ENSG00000174989	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11068204	0.93[EUR][1000 genomes]
rs11068208	0.93[EUR][1000 genomes]
rs11068210	0.93[EUR][1000 genomes]
rs11068212	0.93[EUR][1000 genomes]
rs11068215	0.93[EUR][1000 genomes]
rs11068216	0.93[EUR][1000 genomes]
rs11068217	0.93[EUR][1000 genomes]
rs11068221	0.83[AMR][1000 genomes]
rs11068222	0.83[AMR][1000 genomes]
rs12311024	0.83[AMR][1000 genomes]
rs12311027	0.83[AMR][1000 genomes]
rs12316109	0.83[AMR][1000 genomes]
rs3748264	0.93[EUR][1000 genomes]
rs3809194	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57654988	0.83[AMR][1000 genomes]
rs58117463	0.83[AMR][1000 genomes]
rs73393787	0.83[AMR][1000 genomes]
rs73393789	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73393793	0.83[AMR][1000 genomes]
rs73393795	0.83[AMR][1000 genomes]
rs7958222	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7959242	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9783443	0.93[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	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv826522	chr12:117316379-117317264	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3338350	chr12:117316869-117321167	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117316000-117317400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
2	chr12:117316000-117317800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr12:117316000-117320200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr12:117316200-117317000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
5	chr12:117316200-117317000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
6	chr12:117316200-117317000	Flanking Active TSS	Right Ventricle	heart
7	chr12:117316200-117317000	Bivalent Enhancer	Spleen	Spleen
8	chr12:117316200-117317400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:117316200-117317400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
10	chr12:117316200-117317400	Flanking Bivalent TSS/Enh	NHEK	skin
11	chr12:117316200-117317600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr12:117316200-117317800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr12:117316200-117318000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:117316200-117318400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:117316200-117318600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
16	chr12:117316200-117318800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr12:117316200-117320000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr12:117316200-117320200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:117316200-117320400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr12:117316200-117320400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:117316400-117317000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:117316400-117317000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr12:117316400-117317000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr12:117316400-117317000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:117316400-117317000	Bivalent Enhancer	Fetal Heart	heart
26	chr12:117316400-117317000	Flanking Bivalent TSS/Enh	Placenta	Placenta
27	chr12:117316400-117317000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
28	chr12:117316400-117317000	Active TSS	Hela-S3	cervix
29	chr12:117316400-117317000	Bivalent/Poised TSS	HepG2	liver
30	chr12:117316400-117317200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:117316400-117317200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:117316400-117317200	Bivalent Enhancer	Fetal Lung	lung
33	chr12:117316400-117317400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:117316400-117317400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:117316400-117317400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr12:117316400-117317400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr12:117316400-117317400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr12:117316400-117317400	Bivalent/Poised TSS	Osteobl	bone
39	chr12:117316400-117317600	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
40	chr12:117316400-117317600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:117316400-117317600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
42	chr12:117316400-117317800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:117316400-117317800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:117316400-117317800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:117316400-117317800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr12:117316400-117317800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:117316400-117317800	Enhancers	Liver	Liver
48	chr12:117316400-117317800	Bivalent/Poised TSS	HSMM	muscle
49	chr12:117316400-117318400	Enhancers	Pancreas	Pancrea
50	chr12:117316400-117318600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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