Variant report

Variant	rs6083025
Chromosome Location	chr20:23144070-23144071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2404887	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6076033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076034	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6083026	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6515305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515306	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7269765	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv1066935	chr20:23123507-23146449	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv912817	chr20:23127661-23240969	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv3351449	chr20:23143814-23144120	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6083025	RIN2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23121000-23144200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr20:23137600-23144800	Weak transcription	Ovary	ovary
3	chr20:23138400-23146400	Enhancers	Placenta	Placenta
4	chr20:23139400-23145200	Enhancers	Left Ventricle	heart
5	chr20:23139400-23146600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr20:23139800-23145200	Enhancers	Lung	lung
7	chr20:23139800-23146400	Enhancers	Fetal Muscle Leg	muscle
8	chr20:23139800-23146600	Enhancers	Stomach Mucosa	stomach
9	chr20:23140400-23146400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr20:23140400-23146600	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr20:23140600-23146200	Enhancers	Colonic Mucosa	Colon
12	chr20:23141000-23144200	Enhancers	Adipose Nuclei	Adipose
13	chr20:23141000-23144400	Enhancers	Duodenum Mucosa	Duodenum
14	chr20:23141200-23145400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr20:23141200-23146200	Enhancers	Fetal Muscle Trunk	muscle
16	chr20:23141400-23144800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr20:23141600-23144600	Weak transcription	Brain Hippocampus Middle	brain
18	chr20:23141600-23144800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr20:23142200-23146000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr20:23142200-23146400	Enhancers	Fetal Stomach	stomach
21	chr20:23142800-23146800	Enhancers	Fetal Intestine Large	intestine
22	chr20:23142800-23148000	Weak transcription	NH-A	brain
23	chr20:23143000-23144800	Enhancers	Stomach Smooth Muscle	stomach
24	chr20:23143000-23148000	Weak transcription	NHDF-Ad	bronchial
25	chr20:23143200-23144400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr20:23143200-23144800	Weak transcription	Fetal Lung	lung
27	chr20:23143200-23147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr20:23143400-23145000	Weak transcription	Brain Germinal Matrix	brain
29	chr20:23143400-23146000	Weak transcription	Fetal Heart	heart
30	chr20:23143400-23146200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr20:23143400-23148000	Weak transcription	NHEK	skin
32	chr20:23143600-23144400	Weak transcription	Fetal Intestine Small	intestine
33	chr20:23143600-23145000	Enhancers	Small Intestine	intestine
34	chr20:23143800-23144800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr20:23143800-23144800	Weak transcription	Right Ventricle	heart
36	chr20:23143800-23145000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr20:23143800-23145000	Weak transcription	Psoas Muscle	Psoas
38	chr20:23143800-23145600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr20:23143800-23146000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr20:23143800-23146000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr20:23143800-23147400	Weak transcription	Esophagus	oesophagus
42	chr20:23144000-23145000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr20:23144000-23145000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr20:23144000-23145200	Weak transcription	Gastric	stomach
45	chr20:23144000-23145400	Weak transcription	Spleen	Spleen
46	chr20:23144000-23148400	Weak transcription	Right Atrium	heart
47	chr20:23144000-23150800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr20:23144000-23151000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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