Variant report

Variant	rs6076027
Chromosome Location	chr20:23096273-23096274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23094897..23098917-chr20:23130908..23134771,6	K562	blood:
2	chr20:23095163..23098462-chr20:23100135..23102327,3	K562	blood:
3	chr20:23095049..23097345-chr20:23329449..23331996,2	K562	blood:
4	chr20:23092388..23096498-chr20:23127168..23130418,4	K562	blood:
5	chr20:23095142..23097741-chr20:23111514..23114156,2	K562	blood:
6	chr20:23093195..23094992-chr20:23095074..23097228,2	MCF-7	breast:
7	chr20:23095719..23097726-chr20:23106686..23108284,2	K562	blood:
8	chr20:23092456..23098917-chr20:23127069..23136117,14	K562	blood:
9	chr20:23094758..23097530-chr20:23123211..23126141,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000132661	Chromatin interaction
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];0.82[CHD][hapmap];0.82[MEX][hapmap]
rs17756373	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34151880	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34290000	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4446126	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036310	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]
rs6048548	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6048549	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6076024	0.84[EUR][1000 genomes]
rs6076025	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6076026	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076030	0.85[CEU][hapmap]
rs6083006	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs699794	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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs699795	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];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844814	0.90[ASN][1000 genomes]
rs844815	0.91[ASN][1000 genomes]
rs844816	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs844817	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs844819	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs844821	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs844822	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs844823	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs844825	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs844827	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs844828	0.92[ASN][1000 genomes]
rs844829	0.92[ASN][1000 genomes]
rs844830	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs844831	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs844846	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844850	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs844851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844852	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844853	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844854	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844856	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844860	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844861	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844862	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844863	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844864	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844865	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844866	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844874	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs844877	0.80[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
rs6076027	NUDT22	trans	parietal	SCAN
rs6076027	CST9	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr20:23088200-23096800	Weak transcription	Esophagus	oesophagus
4	chr20:23091200-23100600	Enhancers	Dnd41	blood
5	chr20:23092400-23099600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:23092800-23097600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr20:23093000-23103200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr20:23093200-23096800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr20:23093200-23099000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr20:23093800-23097000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr20:23094600-23096800	Weak transcription	Primary B cells from cord blood	blood
12	chr20:23094600-23097800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr20:23094800-23096600	Enhancers	GM12878-XiMat	blood
14	chr20:23095200-23096800	Weak transcription	Brain Hippocampus Middle	brain
15	chr20:23095200-23100200	Weak transcription	Right Atrium	heart
16	chr20:23095200-23100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr20:23095400-23097000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr20:23095400-23097200	Weak transcription	Spleen	Spleen
19	chr20:23095600-23096600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr20:23095600-23097200	Weak transcription	Adipose Nuclei	Adipose
21	chr20:23095600-23097600	Enhancers	K562	blood
22	chr20:23095600-23099600	Weak transcription	Left Ventricle	heart
23	chr20:23095600-23100000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr20:23095800-23097200	Weak transcription	Fetal Muscle Leg	muscle
25	chr20:23095800-23097800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr20:23096000-23096400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr20:23096000-23097200	Weak transcription	Lung	lung
28	chr20:23096000-23102600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr20:23096200-23096600	Weak transcription	Fetal Thymus	thymus
30	chr20:23096200-23099800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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