Variant report

Variant	rs6036310
Chromosome Location	chr20:23097621-23097622
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23094897..23098917-chr20:23130908..23134771,6	K562	blood:
2	chr20:23072770..23073335-chr20:23096909..23097889,2	MCF-7	breast:
3	chr20:23095163..23098462-chr20:23100135..23102327,3	K562	blood:
4	chr20:23095142..23097741-chr20:23111514..23114156,2	K562	blood:
5	chr20:23095719..23097726-chr20:23106686..23108284,2	K562	blood:
6	chr20:23092456..23098917-chr20:23127069..23136117,14	K562	blood:

Variant related genes	Relation type
ENSG00000233746	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1338945	0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[MEX][hapmap]
rs17756373	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34151880	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34290000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4446126	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048548	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6048549	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6076024	0.84[EUR][1000 genomes]
rs6076025	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6076026	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6076027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6076030	0.85[CEU][hapmap]
rs6083006	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs699794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844814	0.90[ASN][1000 genomes]
rs844815	0.92[ASN][1000 genomes]
rs844816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs844817	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs844819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs844821	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs844822	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs844823	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs844825	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs844827	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs844828	0.93[ASN][1000 genomes]
rs844829	0.93[ASN][1000 genomes]
rs844830	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs844831	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs844846	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs844850	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844852	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844853	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844854	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs844856	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844860	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844861	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844862	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844863	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844864	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844865	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844866	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844874	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs844877	0.88[AMR][1000 genomes];0.93[EUR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6036310	NUDT22	trans	parietal	SCAN
rs6036310	CST9	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23085800-23114600	Enhancers	Placenta	Placenta
2	chr20:23088000-23100000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr20:23091200-23100600	Enhancers	Dnd41	blood
4	chr20:23092400-23099600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:23093000-23103200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr20:23093200-23099000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr20:23094600-23097800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr20:23095200-23100200	Weak transcription	Right Atrium	heart
9	chr20:23095200-23100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr20:23095600-23099600	Weak transcription	Left Ventricle	heart
11	chr20:23095600-23100000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr20:23095800-23097800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr20:23096000-23102600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr20:23096200-23099800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr20:23096400-23097800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr20:23096600-23097800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr20:23096600-23098000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:23096600-23098000	Enhancers	NHEK	skin
19	chr20:23096600-23098800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:23096600-23099000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr20:23096800-23097800	Enhancers	Primary B cells from cord blood	blood
22	chr20:23096800-23097800	Enhancers	HMEC	breast
23	chr20:23096800-23098000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr20:23096800-23098000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:23096800-23098800	Enhancers	Esophagus	oesophagus
26	chr20:23097000-23097800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr20:23097000-23098000	Enhancers	NHDF-Ad	bronchial
28	chr20:23097000-23098800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr20:23097200-23097800	Enhancers	Adipose Nuclei	Adipose
30	chr20:23097200-23098000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:23097200-23100000	Enhancers	Lung	lung
32	chr20:23097200-23100000	Enhancers	GM12878-XiMat	blood
33	chr20:23097200-23100800	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr20:23097200-23102000	Enhancers	Fetal Muscle Leg	muscle
35	chr20:23097400-23097800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr20:23097400-23097800	Enhancers	HUVEC	blood vessel
37	chr20:23097400-23099600	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr20:23097400-23100000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr20:23097400-23100000	Weak transcription	Brain Hippocampus Middle	brain
40	chr20:23097400-23100200	Weak transcription	Fetal Thymus	thymus
41	chr20:23097600-23098800	Weak transcription	Spleen	Spleen
42	chr20:23097600-23099200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr20:23097600-23099400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr20:23097600-23099400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr20:23097600-23100200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr20:23097600-23101400	Weak transcription	K562	blood
47	chr20:23097600-23110200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links