Variant report

Variant	rs60297652
Chromosome Location	chr12:56224366-56224367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:215)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:215 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56223120-56224751	HEK293	kidney:	n/a	n/a
2	POLR2A	chr12:56222883-56224839	GM18505	blood:	n/a	n/a
3	POLR2A	chr12:56223209-56225353	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr12:56223086-56224836	Raji	blood:	n/a	n/a
5	TAF1	chr12:56224078-56224790	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:56224346-56224855	GM12892	blood:	n/a	n/a
7	SP1	chr12:56224156-56224789	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr12:56223136-56225011	HCT-116	colon:	n/a	chr12:56223349-56223363 chr12:56223348-56223360
9	SP1	chr12:56224257-56225035	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOSL2	chr12:56224355-56224804	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:56222695-56224993	ECC-1	luminal epithelium:	n/a	n/a
12	SIN3A	chr12:56223218-56225194	H1-hESC	embryonic stem cell:	n/a	chr12:56223337-56223350
13	POLR2A	chr12:56222788-56225023	HepG2	liver:	n/a	n/a
14	NFIC	chr12:56223167-56224740	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr12:56223844-56224826	HepG2	liver:	n/a	n/a
16	BHLHE40	chr12:56224193-56224776	K562	blood:	n/a	n/a
17	EP300	chr12:56224284-56224669	GM12878	blood:	n/a	n/a
18	MAZ	chr12:56222508-56225685	IMR90	lung:	n/a	chr12:56225419-56225428
19	POLR2A	chr12:56222943-56224986	MCF-7	breast:	n/a	n/a
20	ELF1	chr12:56222705-56224939	GM12878	blood:	n/a	chr12:56223420-56223429 chr12:56223389-56223401 chr12:56223343-56223355 chr12:56224404-56224417 chr12:56223419-56223430 chr12:56223419-56223430
21	EGR1	chr12:56224282-56224720	H1-hESC	embryonic stem cell:	n/a	n/a
22	JUND	chr12:56223254-56224849	K562	blood:	n/a	n/a
23	POLR2A	chr12:56223177-56224366	HL-60	blood:	n/a	n/a
24	SMARCB1	chr12:56222779-56224636	Hela-S3	cervix:	n/a	n/a
25	SP1	chr12:56224344-56224704	GM12878	blood:	n/a	n/a
26	ZC3H11A	chr12:56224167-56224539	K562	blood:	n/a	n/a
27	GABPA	chr12:56224192-56224750	A549	lung:	n/a	n/a
28	POLR2A	chr12:56223875-56224447	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUN	chr12:56224354-56224752	K562	blood:	n/a	chr12:56224571-56224584
30	CREB1	chr12:56224330-56224823	H1-hESC	embryonic stem cell:	n/a	n/a
31	TCF12	chr12:56223054-56225003	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr12:56223063-56224938	GM12878	blood:	n/a	n/a
33	RAD21	chr12:56224125-56224386	Hela-S3	cervix:	n/a	n/a
34	MAX	chr12:56223194-56224834	MCF-7	breast:	n/a	n/a
35	SP1	chr12:56223173-56225027	HCT-116	colon:	n/a	chr12:56223349-56223363 chr12:56223348-56223360
36	RAD21	chr12:56224013-56225083	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr12:56223126-56224831	GM12892	blood:	n/a	n/a
38	ZBTB7A	chr12:56223946-56224661	K562	blood:	n/a	n/a
39	TAF1	chr12:56223290-56224902	H1-neurons	neurons:	n/a	n/a
40	CTBP2	chr12:56223388-56224938	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr12:56220836-56225418	SK-N-MC	brain:	n/a	n/a
42	BACH1	chr12:56223960-56224774	H1-hESC	embryonic stem cell:	n/a	n/a
43	FOXM1	chr12:56223924-56224755	GM12878	blood:	n/a	n/a
44	NFIC	chr12:56224282-56224643	HepG2	liver:	n/a	n/a
45	SP1	chr12:56223047-56224832	A549	lung:	n/a	chr12:56223349-56223363 chr12:56223348-56223360
46	CHD1	chr12:56222324-56225296	IMR90	lung:	n/a	n/a
47	PML	chr12:56223053-56224993	GM12878	blood:	n/a	n/a
48	MAX	chr12:56224329-56224879	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr12:56224366-56225007	U87	brain:	n/a	n/a
50	CREB1	chr12:56224198-56224938	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56222205..56224922-chr12:56358822..56360561,2	MCF-7	breast:
2	chr12:56222874..56225459-chr12:56331362..56334369,4	MCF-7	breast:
3	chr12:56222506..56227501-chr12:56233677..56237355,4	K562	blood:
4	chr12:56222034..56224424-chr12:56351051..56353709,2	MCF-7	breast:
5	chr12:56222083..56225232-chr12:56434095..56438071,8	MCF-7	breast:
6	chr12:56222395..56225334-chr12:56325812..56327785,2	K562	blood:
7	chr12:56119665..56125098-chr12:56220794..56225708,11	MCF-7	breast:
8	chr12:56217816..56225905-chr12:56319649..56327312,13	K562	blood:
9	chr12:53454054..53456041-chr12:56223031..56224851,2	MCF-7	breast:
10	chr12:56222158..56225126-chr12:56264832..56267063,2	MCF-7	breast:
11	chr12:56223504..56226231-chr17:81007851..81010191,2	MCF-7	breast:
12	chr12:56221380..56224964-chr12:56389518..56391626,4	MCF-7	breast:
13	chr12:56223221..56225412-chr12:56473813..56476164,2	MCF-7	breast:
14	chr12:56217992..56226798-chr12:56311494..56331042,68	MCF-7	breast:
15	chr12:56219783..56227072-chr12:56318292..56323886,14	K562	blood:
16	chr12:56223309..56224865-chr12:56552081..56554400,2	MCF-7	breast:
17	chr12:56221995..56224652-chr12:56472013..56474310,2	MCF-7	breast:
18	chr12:56222536..56225150-chr12:56365763..56368658,3	MCF-7	breast:
19	chr12:56222623..56225394-chr12:56346640..56348578,2	K562	blood:
20	chr12:56222332..56225809-chr12:56227507..56233140,8	K562	blood:
21	chr12:56221810..56225034-chr12:56267373..56269273,5	MCF-7	breast:
22	chr12:56223489..56225123-chr12:120729233..120730868,2	MCF-7	breast:
23	chr11:64884402..64886500-chr12:56223721..56226196,2	MCF-7	breast:
24	chr12:56115949..56118195-chr12:56224037..56226803,2	MCF-7	breast:
25	chr12:56222612..56225517-chr12:56372520..56376647,5	MCF-7	breast:
26	chr12:56221098..56224816-chr12:56434415..56439287,4	MCF-7	breast:
27	chr12:56217492..56232243-chr12:56318854..56330686,48	MCF-7	breast:
28	chr12:56223409..56227527-chr12:56348845..56352516,3	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ORMDL2-1	chr12:56223744-56224867	NONHSAT028687
2	lnc-ORMDL2-1	chr12:56223744-56224867	NONHSAT028689
3	lnc-ORMDL2-1	chr12:56224156-56224867	NONHSAT028692
4	lnc-ORMDL2-1	chr12:56224156-56224867	NONHSAT028693
5	lnc-ORMDL2-1	chr12:56223744-56225327	NONHSAT028691

No data

Variant related genes	Relation type
DNAJC14	TF binding region
ENSG00000257390	TF binding region
TMEM198B	TF binding region
ENSG00000207339	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000135437	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000175711	Chromatin interaction
ENSG00000237493	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000111077	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000257966	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000123342	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13020	1.00[ASN][1000 genomes]
rs17117976	1.00[ASN][1000 genomes]
rs17844785	1.00[ASN][1000 genomes]
rs17844786	1.00[ASN][1000 genomes]
rs17844787	1.00[ASN][1000 genomes]
rs2231467	1.00[ASN][1000 genomes]
rs6581081	1.00[ASN][1000 genomes]
rs715817	1.00[ASN][1000 genomes]
rs772258	1.00[ASN][1000 genomes]
rs7975037	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56220000-56225400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:56222200-56224400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:56222200-56225000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr12:56222400-56224400	Active TSS	Colonic Mucosa	Colon
5	chr12:56222400-56224800	Active TSS	NHLF	lung
6	chr12:56222400-56225000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:56222400-56225000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:56222400-56225000	Active TSS	Right Ventricle	heart
9	chr12:56222400-56225400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:56222400-56225600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr12:56222400-56225600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:56222600-56224600	Active TSS	K562	blood
13	chr12:56222600-56224800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:56222600-56224800	Active TSS	Lung	lung
15	chr12:56222600-56224800	Active TSS	GM12878-XiMat	blood
16	chr12:56222600-56224800	Active TSS	HSMM	muscle
17	chr12:56222600-56225000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr12:56222600-56225000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:56222600-56225000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:56222600-56225000	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr12:56222600-56225000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr12:56222600-56225000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:56222600-56225000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:56222600-56225000	Active TSS	Brain Anterior Caudate	brain
25	chr12:56222600-56225000	Active TSS	Esophagus	oesophagus
26	chr12:56222600-56225000	Active TSS	Fetal Intestine Small	intestine
27	chr12:56222600-56225000	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr12:56222600-56225200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:56222600-56225200	Active TSS	Brain Angular Gyrus	brain
30	chr12:56222600-56225200	Active TSS	Left Ventricle	heart
31	chr12:56222600-56225400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr12:56222600-56225400	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:56222600-56225400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:56222600-56225400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr12:56222600-56225400	Active TSS	HSMMtube	muscle
36	chr12:56222600-56225600	Active TSS	Fetal Kidney	kidney
37	chr12:56222600-56225600	Active TSS	NHDF-Ad	bronchial
38	chr12:56222600-56226000	Active TSS	Rectal Smooth Muscle	rectum
39	chr12:56222800-56224400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:56222800-56224400	Active TSS	Muscle Satellite Cultured Cells	--
41	chr12:56222800-56224400	Active TSS	Osteobl	bone
42	chr12:56222800-56224600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:56222800-56224600	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr12:56222800-56224600	Active TSS	Spleen	Spleen
45	chr12:56222800-56224600	Active TSS	A549	lung
46	chr12:56222800-56224600	Active TSS	HUVEC	blood vessel
47	chr12:56222800-56224800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:56222800-56224800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:56222800-56224800	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr12:56222800-56224800	Active TSS	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links