Variant report

Variant	rs6862424
Chromosome Location	chr5:54179467-54179468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:54166309..54167932-chr5:54178530..54180323,2	K562	blood:
2	chr5:54173158..54177091-chr5:54177548..54180449,4	K562	blood:

Variant related genes	Relation type
ENSG00000249843	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10037462	1.00[AMR][1000 genomes]
rs10045193	1.00[AMR][1000 genomes]
rs10065443	1.00[AMR][1000 genomes]
rs10075204	1.00[AMR][1000 genomes]
rs10075516	1.00[AMR][1000 genomes]
rs10213818	1.00[AMR][1000 genomes]
rs13353863	1.00[AMR][1000 genomes]
rs13356362	1.00[AMR][1000 genomes]
rs13359248	1.00[AMR][1000 genomes]
rs1560168	1.00[AMR][1000 genomes]
rs28585462	1.00[AMR][1000 genomes]
rs6861370	1.00[AMR][1000 genomes]
rs6880497	1.00[AMR][1000 genomes]
rs7708519	1.00[AMR][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	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv598179	chr5:54156269-54192823	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54178600-54179600	Bivalent Enhancer	HMEC	breast
2	chr5:54178800-54179600	Flanking Active TSS	NHEK	skin
3	chr5:54178800-54179800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
4	chr5:54178800-54180400	Bivalent Enhancer	Fetal Brain Male	brain
5	chr5:54179000-54179600	Bivalent/Poised TSS	Colonic Mucosa	Colon
6	chr5:54179000-54179600	Enhancers	Lung	lung
7	chr5:54179000-54179600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
8	chr5:54179000-54179800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:54179000-54179800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
10	chr5:54179000-54180000	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr5:54179000-54180200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr5:54179000-54180200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
13	chr5:54179000-54180200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:54179000-54180400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr5:54179000-54180400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr5:54179000-54180400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr5:54179000-54180400	Active TSS	Colon Smooth Muscle	Colon
18	chr5:54179200-54179600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:54179200-54179600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
20	chr5:54179200-54179600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
21	chr5:54179200-54179600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
22	chr5:54179200-54179600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:54179200-54179600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:54179200-54179600	Flanking Bivalent TSS/Enh	Liver	Liver
25	chr5:54179200-54179600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
26	chr5:54179200-54179600	Active TSS	Fetal Kidney	kidney
27	chr5:54179200-54179600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
28	chr5:54179200-54179600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
29	chr5:54179200-54179600	Active TSS	Right Ventricle	heart
30	chr5:54179200-54179600	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
31	chr5:54179200-54179600	Flanking Bivalent TSS/Enh	NH-A	brain
32	chr5:54179200-54179600	Flanking Active TSS	NHLF	lung
33	chr5:54179200-54179600	Flanking Bivalent TSS/Enh	Osteobl	bone
34	chr5:54179200-54179800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
35	chr5:54179200-54179800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
36	chr5:54179200-54179800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:54179200-54179800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
38	chr5:54179200-54179800	Flanking Bivalent TSS/Enh	Placenta	Placenta
39	chr5:54179200-54179800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
40	chr5:54179200-54180000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr5:54179200-54180000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:54179200-54180000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:54179200-54180000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:54179200-54180000	Active TSS	Aorta	Aorta
45	chr5:54179200-54180000	Active TSS	Brain Anterior Caudate	brain
46	chr5:54179200-54180000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
47	chr5:54179200-54180000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
48	chr5:54179200-54180000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
49	chr5:54179200-54180000	Active TSS	Ovary	ovary
50	chr5:54179200-54180000	Flanking Active TSS	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links