Variant report

Variant	rs35985500
Chromosome Location	chr12:58289281-58289282
allele	C/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	POLR2A	chr12:58288646-58291559	SK-N-MC	brain:	n/a	n/a
2	CEBPB	chr12:58289264-58289558	K562	blood:	n/a	chr12:58289410-58289421
3	CEBPB	chr12:58289266-58289599	HepG2	liver:	n/a	chr12:58289410-58289421
4	CEBPB	chr12:58289277-58289564	Hela-S3	cervix:	n/a	chr12:58289410-58289421
5	ZNF263	chr12:58289136-58289767	HEK293-T-REx	kidney:	n/a	chr12:58289281-58289302
6	MAZ	chr12:58289185-58291043	IMR90	lung:	n/a	chr12:58290564-58290577

No.	Distal block	Cell Line	Cell type
1	chr12:58283503..58285277-chr12:58287800..58289369,2	K562	blood:
2	chr12:58238695..58240382-chr12:58287823..58289916,2	K562	blood:
3	chr12:58236711..58242486-chr12:58286970..58293951,15	MCF-7	breast:
4	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTDSP2-1	chr12:58287523-58290265	ENSG00000245651
2	lnc-CTDSP2-1	chr12:58287523-58290267	XLOC_010101
3	lnc-CTDSP2-1	chr12:58287523-58290265	ENSG00000245651

Variant related genes	Relation type
ENSG00000245651	TF binding region
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11172376	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172377	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11834260	0.95[ASN][1000 genomes]
rs12296922	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309291	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12322495	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322586	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17119981	0.95[ASN][1000 genomes]
rs17119991	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34241380	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34372362	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35441007	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61935768	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58282200-58289600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:58285600-58290000	Enhancers	Brain Angular Gyrus	brain
3	chr12:58285600-58290000	Enhancers	Left Ventricle	heart
4	chr12:58285600-58290200	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr12:58285800-58289600	Enhancers	Duodenum Mucosa	Duodenum
6	chr12:58285800-58289800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:58285800-58290000	Enhancers	Placenta	Placenta
8	chr12:58285800-58290000	Enhancers	Right Atrium	heart
9	chr12:58285800-58290000	Enhancers	Right Ventricle	heart
10	chr12:58285800-58290200	Enhancers	Lung	lung
11	chr12:58286000-58289800	Enhancers	Stomach Mucosa	stomach
12	chr12:58286000-58290600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:58286200-58289400	Enhancers	Brain Cingulate Gyrus	brain
14	chr12:58286200-58290000	Enhancers	Fetal Thymus	thymus
15	chr12:58286400-58289800	Enhancers	Brain Substantia Nigra	brain
16	chr12:58286600-58289600	Enhancers	Fetal Brain Female	brain
17	chr12:58286600-58290200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr12:58286800-58289800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:58286800-58291400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:58287000-58289600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:58287000-58289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:58287000-58290000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:58287200-58290000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr12:58287200-58290000	Enhancers	Pancreas	Pancrea
25	chr12:58287200-58290000	Enhancers	Psoas Muscle	Psoas
26	chr12:58287200-58290000	Enhancers	NH-A	brain
27	chr12:58287200-58290200	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr12:58287400-58290000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:58287400-58290000	Enhancers	Primary hematopoietic stem cells	blood
30	chr12:58287600-58289400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:58287600-58289800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:58287600-58289800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr12:58287600-58290000	Enhancers	Primary B cells from peripheral blood	blood
34	chr12:58287600-58290000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:58287800-58289800	Enhancers	Brain Hippocampus Middle	brain
36	chr12:58287800-58290000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:58287800-58290000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:58287800-58290400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:58287800-58290400	Flanking Active TSS	NHDF-Ad	bronchial
40	chr12:58288000-58289800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:58288000-58289800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:58288000-58289800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:58288000-58290000	Enhancers	Colonic Mucosa	Colon
44	chr12:58288000-58290200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:58288200-58289400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:58288200-58289600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr12:58288200-58289600	Enhancers	Gastric	stomach
48	chr12:58288200-58289800	Enhancers	Aorta	Aorta
49	chr12:58288200-58289800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:58288200-58289800	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links