Variant report

Variant	rs6871676
Chromosome Location	chr5:80598969-80598970
allele	C/T
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	CEBPB	chr5:80598823-80598977	K562	blood:	n/a	chr5:80598904-80598915
2	POLR2A	chr5:80598951-80598980	MCF-7	breast:	n/a	n/a
3	CEBPB	chr5:80598809-80599027	HepG2	liver:	n/a	chr5:80598904-80598915

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80598755..80600911-chr5:80604785..80606382,2	K562	blood:

Variant related genes	Relation type
CKMT2-AS1	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10041138	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10052929	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10061143	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12514420	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13172928	0.82[ASN][1000 genomes]
rs1566433	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2406557	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4502795	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4704711	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4704713	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4704714	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57040652	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57266451	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6863732	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6868743	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6877340	0.82[ASN][1000 genomes]
rs6889795	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6896441	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7718501	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs955948	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80593800-80599800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:80598000-80599800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:80598000-80605200	Weak transcription	Ovary	ovary
4	chr5:80598200-80599000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:80598200-80599600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:80598200-80612400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:80598400-80599000	Enhancers	Fetal Heart	heart
8	chr5:80598400-80599200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr5:80598400-80599200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr5:80598400-80599400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:80598400-80599600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr5:80598400-80599600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:80598400-80599800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:80598400-80600600	Weak transcription	Colonic Mucosa	Colon
15	chr5:80598400-80600600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:80598400-80600600	Weak transcription	Thymus	Thymus
17	chr5:80598400-80601200	Weak transcription	Esophagus	oesophagus
18	chr5:80598400-80604800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:80598400-80605200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:80598400-80606800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:80598400-80606800	Weak transcription	Right Ventricle	heart
22	chr5:80598400-80611200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:80598600-80599000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:80598600-80599000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:80598600-80599000	Enhancers	Adipose Nuclei	Adipose
26	chr5:80598600-80599000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr5:80598600-80599000	Enhancers	Brain Substantia Nigra	brain
28	chr5:80598600-80599000	Weak transcription	Pancreas	Pancrea
29	chr5:80598600-80599200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr5:80598600-80599200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr5:80598600-80599400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr5:80598600-80599400	Enhancers	Fetal Lung	lung
33	chr5:80598600-80599600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr5:80598600-80599600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr5:80598600-80599800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:80598600-80599800	Enhancers	Primary T cells from cord blood	blood
37	chr5:80598600-80599800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr5:80598600-80599800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr5:80598600-80599800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr5:80598600-80599800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:80598600-80599800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr5:80598600-80600000	Enhancers	NH-A	brain
43	chr5:80598600-80600200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr5:80598600-80600200	Enhancers	Liver	Liver
45	chr5:80598600-80600200	Enhancers	HMEC	breast
46	chr5:80598600-80600200	Enhancers	Osteobl	bone
47	chr5:80598600-80600400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:80598600-80600600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:80598600-80600600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:80598600-80600600	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links