Variant report

Variant	rs6558569
Chromosome Location	chr8:1932328-1932329
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:1920801..1923588-chr8:1929639..1933248,3	MCF-7	breast:
2	chr1:8021103..8021603-chr8:1931796..1932353,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000270988	Chromatin interaction
ENSG00000176595	Chromatin interaction
ENSG00000253764	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10088130	0.83[EUR][1000 genomes]
rs10098493	0.99[EUR][1000 genomes]
rs10105508	0.84[EUR][1000 genomes]
rs10780156	0.83[EUR][1000 genomes]
rs11785522	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11997759	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12676812	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3087819	0.83[EUR][1000 genomes]
rs4322044	0.84[EUR][1000 genomes]
rs4357331	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4410948	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4532639	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4541975	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62478221	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6558575	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7018066	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7386983	0.83[EUR][1000 genomes]
rs7460119	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889704	chr8:1563904-1965389	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv889708	chr8:1581839-1965389	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv889709	chr8:1581839-1965389	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv889712	chr8:1591412-2337777	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv889714	chr8:1616718-1965389	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv609531	chr8:1717036-1965389	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv889724	chr8:1756800-1965389	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv889729	chr8:1800560-1947417	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv889731	chr8:1868842-1965389	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv889736	chr8:1892069-1965389	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv889738	chr8:1897249-1965389	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv824473	chr8:1914305-1965389	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv824474	chr8:1915145-1960212	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv824477	chr8:1915145-1965389	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv889740	chr8:1916347-1954464	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv889741	chr8:1916347-1955283	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv889742	chr8:1918352-1955142	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1015930	chr8:1919596-1952936	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	esv1839364	chr8:1920461-1951163	Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1019578	chr8:1926059-1965389	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1923800-1939800	Weak transcription	Colonic Mucosa	Colon
2	chr8:1924000-1939600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr8:1924400-1939200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr8:1924800-1936800	Weak transcription	Brain Angular Gyrus	brain
5	chr8:1925000-1933800	Weak transcription	Brain Anterior Caudate	brain
6	chr8:1929000-1932800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr8:1929000-1933000	Weak transcription	Psoas Muscle	Psoas
8	chr8:1929000-1933200	Weak transcription	Fetal Stomach	stomach
9	chr8:1929200-1932800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr8:1929200-1933800	Weak transcription	Brain Substantia Nigra	brain
11	chr8:1929200-1937800	Weak transcription	Right Atrium	heart
12	chr8:1929200-1939400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr8:1929200-1940200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr8:1929400-1933000	Weak transcription	Fetal Brain Female	brain
15	chr8:1929400-1933400	Weak transcription	Fetal Muscle Leg	muscle
16	chr8:1929400-1940000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:1929400-1947800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr8:1929600-1933600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr8:1929600-1933800	Weak transcription	Brain Hippocampus Middle	brain
20	chr8:1929600-1934000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:1930000-1932800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr8:1930000-1939800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr8:1930800-1939800	Weak transcription	Fetal Intestine Large	intestine
24	chr8:1931200-1933000	Strong transcription	Fetal Intestine Small	intestine
25	chr8:1931400-1933200	Weak transcription	Dnd41	blood
26	chr8:1931400-1940000	Weak transcription	Primary T cells from cord blood	blood
27	chr8:1931600-1937200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr8:1931600-1939600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr8:1931800-1932600	Weak transcription	Thymus	Thymus
30	chr8:1931800-1932800	Weak transcription	Fetal Thymus	thymus
31	chr8:1931800-1937600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr8:1931800-1939400	Weak transcription	Lung	lung
33	chr8:1931800-1939600	Weak transcription	Right Ventricle	heart
34	chr8:1931800-1948800	Weak transcription	Brain Germinal Matrix	brain
35	chr8:1932000-1932400	Weak transcription	Pancreas	Pancrea
36	chr8:1932000-1939800	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links