Variant report

Variant	rs58990065
Chromosome Location	chr12:42678447-42678448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr12:42677957-42678542	HL-60	blood:	n/a	chr12:42678153-42678166 chr12:42678154-42678167 chr12:42678156-42678165 chr12:42678153-42678166
2	SPI1	chr12:42677681-42678663	GM12878	blood:	n/a	chr12:42678153-42678166 chr12:42678154-42678167 chr12:42678156-42678165 chr12:42678153-42678166

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:42678439-42678489	LNCaP	prostate:	n/a
2	chr12:42678439-42678489	HCM	heart:	n/a
3	chr12:42678439-42678489	NHBE	bronchial:	n/a
4	chr12:42678439-42678489	ovcar-3	ovarian:	n/a
5	chr12:42678439-42678489	GM12891	blood:	n/a
6	chr12:42678439-42678489	NHDF-neo	bronchial:	n/a
7	chr12:42678439-42678489	NH-A	brain:	n/a
8	chr12:42678439-42678489	HCPEpiC	choroid plexus:	n/a
9	chr12:42678439-42678489	HUVEC	blood vessel:	n/a
10	chr12:42678439-42678489	PFSK-1	brain:	n/a
11	chr12:42678439-42678489	H1-hESC	embryonic stem cell:	embryo
12	chr12:42678439-42678489	HNPCEpiC	eye:	n/a
13	chr12:42678439-42678489	SKMC	muscle:	n/a
14	chr12:42678439-42678489	GM19239	blood:	n/a
15	chr12:42678439-42678489	GM06990	blood:	n/a
16	chr12:42678439-42678489	HRCEpiC	kidney:	n/a
17	chr12:42678439-42678489	HAEpiC	amniotic membrane:	n/a
18	chr12:42678439-42678489	HMEC	breast:	n/a
19	chr12:42678439-42678489	HCT-116	colon:	n/a
20	chr12:42678439-42678489	ProgFib	skin:	n/a
21	chr12:42678439-42678489	U87	brain:	n/a
22	chr12:42678439-42678489	IMR90	lung:	fetal
23	chr12:42678439-42678489	AG10803	skin:	n/a
24	chr12:42678439-42678489	SK-N-MC	brain:	n/a
25	chr12:42678439-42678489	PANC-1	pancreas:	n/a
26	chr12:42678439-42678489	GM12878	blood:	n/a
27	chr12:42678439-42678489	Caco-2	colon:	n/a
28	chr12:42678439-42678489	PrEC	prostate:	n/a
29	chr12:42678439-42678489	RPTEC	kidney:	n/a
30	chr12:42678439-42678489	SK-N-SH	brain:	n/a
31	chr12:42678439-42678489	AG09319	gingival:	n/a
32	chr12:42678439-42678489	AG04450	lung:	fetal
33	chr12:42678439-42678489	NB4	blood:	n/a
34	chr12:42678439-42678489	HIPEpiC	eye:	n/a
35	chr12:42678439-42678489	HepG2	liver:	n/a
36	chr12:42678439-42678489	AG04449	skin:	fetal
37	chr12:42678439-42678489	SAEC	small airway:	n/a
38	chr12:42678439-42678489	SK-N-SH_RA	brain:	n/a
39	chr12:42678439-42678489	T-47D	breast:	n/a
40	chr12:42678439-42678489	K562	blood:	n/a
41	chr12:42678439-42678489	HL-60	blood:	n/a
42	chr12:42678439-42678489	HEK293	kidney:	embryo
43	chr12:42678439-42678489	HCF	heart:	n/a
44	chr12:42678439-42678489	Hela-S3	cervix:	n/a
45	chr12:42678439-42678489	MCF-7	breast:	n/a
46	chr12:42678439-42678489	Hepatocyte	liver:	n/a
47	chr12:42678439-42678489	CMK	blood:	n/a
48	chr12:42678439-42678489	BE2_C	brain:	n/a
49	chr12:42678439-42678489	HPAEpiC	pulmonary alveolar:	n/a
50	chr12:42678439-42678489	HRPEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42628933..42631905-chr12:42678028..42680094,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257674	TF binding region
ENSG00000257674	CpG island
ENSG00000015153	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17091037	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17091040	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17091078	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs17091110	0.80[ASN][1000 genomes]
rs17091127	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs17091132	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs34837068	0.81[AFR][1000 genomes]
rs56687376	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42677000-42678600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:42677400-42678600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr12:42677600-42678600	Enhancers	GM12878-XiMat	blood
4	chr12:42677600-42678800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:42677600-42678800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:42677800-42678600	Enhancers	Primary hematopoietic stem cells	blood
7	chr12:42678000-42678600	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr12:42678000-42679200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links