Variant report

Variant	rs6083009
Chromosome Location	chr20:23107438-23107439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23105413..23107552-chr20:23159018..23161237,2	K562	blood:
2	chr20:23088338..23089890-chr20:23107180..23109300,2	MCF-7	breast:
3	chr20:23106418..23109174-chr20:23126935..23129451,2	K562	blood:
4	chr20:23103623..23110911-chr20:23111294..23114699,12	K562	blood:
5	chr20:23099426..23103463-chr20:23105068..23107847,3	K562	blood:
6	chr20:23095719..23097726-chr20:23106686..23108284,2	K562	blood:

Variant related genes	Relation type
ENSG00000233746	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs13045861	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083010	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083012	0.92[CEU][hapmap];0.87[AMR][1000 genomes]
rs6083013	0.86[CHB][hapmap]
rs6083014	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs6083015	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs6132568	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6137837	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844828	0.84[EUR][1000 genomes]
rs844829	0.84[EUR][1000 genomes]
rs844903	0.86[CHB][hapmap]
rs946369	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs946371	0.91[CHB][hapmap];0.81[JPT][hapmap]

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	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6083009	CST9	cis	cerebellum	SCAN
rs6083009	RIN2	cis	parietal	SCAN
rs6083009	CST8	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23085800-23114600	Enhancers	Placenta	Placenta
2	chr20:23097600-23110200	Weak transcription	Pancreas	Pancrea
3	chr20:23100200-23111200	Enhancers	Fetal Thymus	thymus
4	chr20:23101200-23109400	Weak transcription	Liver	Liver
5	chr20:23101800-23109200	Weak transcription	Right Ventricle	heart
6	chr20:23102000-23114000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr20:23103200-23109800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:23104000-23108000	Enhancers	Fetal Muscle Trunk	muscle
9	chr20:23104600-23111600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr20:23105000-23109800	Enhancers	Brain Hippocampus Middle	brain
11	chr20:23105200-23109200	Weak transcription	Fetal Lung	lung
12	chr20:23105200-23111000	Enhancers	Fetal Muscle Leg	muscle
13	chr20:23105400-23107600	Enhancers	K562	blood
14	chr20:23105400-23107800	Flanking Active TSS	Dnd41	blood
15	chr20:23105600-23108600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr20:23105800-23107600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr20:23105800-23107600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr20:23105800-23107600	Enhancers	GM12878-XiMat	blood
19	chr20:23105800-23107600	Enhancers	NHLF	lung
20	chr20:23105800-23108200	Enhancers	Psoas Muscle	Psoas
21	chr20:23105800-23108400	Enhancers	Lung	lung
22	chr20:23105800-23108600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr20:23105800-23110000	Enhancers	Primary B cells from cord blood	blood
24	chr20:23105800-23110000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr20:23105800-23111000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr20:23106000-23107600	Enhancers	Left Ventricle	heart
27	chr20:23106000-23108000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr20:23106000-23108000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr20:23106000-23112000	Enhancers	Adipose Nuclei	Adipose
30	chr20:23106200-23110200	Weak transcription	Fetal Intestine Small	intestine
31	chr20:23106400-23107800	Enhancers	Primary B cells from peripheral blood	blood
32	chr20:23106400-23108200	Enhancers	Primary hematopoietic stem cells	blood
33	chr20:23106400-23108400	Enhancers	Fetal Stomach	stomach
34	chr20:23106400-23108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr20:23106400-23109600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr20:23106600-23107600	Weak transcription	Brain Anterior Caudate	brain
37	chr20:23106600-23107800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr20:23106600-23108200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr20:23106600-23109800	Weak transcription	Right Atrium	heart
40	chr20:23106600-23111000	Enhancers	Spleen	Spleen
41	chr20:23106600-23112600	Weak transcription	Fetal Intestine Large	intestine
42	chr20:23106800-23107600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr20:23106800-23109800	Weak transcription	Colonic Mucosa	Colon
44	chr20:23106800-23110800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr20:23106800-23114400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr20:23106800-23116400	Weak transcription	Esophagus	oesophagus
47	chr20:23107000-23108600	Weak transcription	Brain Substantia Nigra	brain
48	chr20:23107200-23109200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr20:23107200-23110800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr20:23107400-23107600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links