Variant report

Variant	rs17805665
Chromosome Location	chr4:74472268-74472269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11736697	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247583	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs13131954	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13142786	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1534642	0.88[CEU][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1957659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957660	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2010987	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446944	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1008104	chr4:74468434-74621952	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17805665	CNOT6L	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74440200-74472600	Weak transcription	Gastric	stomach
2	chr4:74463800-74474200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:74464200-74476400	Enhancers	Stomach Mucosa	stomach
4	chr4:74464200-74477200	Enhancers	Fetal Intestine Small	intestine
5	chr4:74465000-74475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:74465400-74483000	Weak transcription	Esophagus	oesophagus
7	chr4:74465800-74472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:74465800-74473000	Weak transcription	NHEK	skin
9	chr4:74465800-74476000	Weak transcription	Placenta	Placenta
10	chr4:74466800-74474600	Weak transcription	Fetal Kidney	kidney
11	chr4:74467000-74474400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:74469400-74474400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:74469800-74473000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:74469800-74473000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:74469800-74474400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:74469800-74474400	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:74469800-74474600	Weak transcription	Liver	Liver
18	chr4:74469800-74477200	Enhancers	HepG2	liver
19	chr4:74470000-74472600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:74470000-74473000	Weak transcription	Osteobl	bone
21	chr4:74470000-74474400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:74470000-74475400	Weak transcription	Fetal Lung	lung
23	chr4:74470000-74475400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:74470800-74473600	Enhancers	Primary B cells from peripheral blood	blood
25	chr4:74470800-74473600	Enhancers	Primary T cells from cord blood	blood
26	chr4:74470800-74476000	Enhancers	Fetal Intestine Large	intestine
27	chr4:74471000-74472600	Enhancers	Dnd41	blood
28	chr4:74471000-74473200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:74471200-74472800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr4:74471200-74473400	Enhancers	Primary B cells from cord blood	blood
31	chr4:74471400-74472800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:74471600-74473400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:74471800-74472400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr4:74471800-74472400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:74471800-74472800	Flanking Active TSS	Thymus	Thymus
36	chr4:74471800-74473200	Enhancers	Small Intestine	intestine
37	chr4:74471800-74473400	Enhancers	Duodenum Mucosa	Duodenum
38	chr4:74472000-74472400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:74472000-74472400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr4:74472000-74472400	Flanking Active TSS	Fetal Thymus	thymus
41	chr4:74472000-74472400	Weak transcription	HSMM	muscle
42	chr4:74472000-74473400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:74472000-74473400	Flanking Active TSS	GM12878-XiMat	blood
44	chr4:74472000-74473600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr4:74472000-74473800	Enhancers	Pancreas	Pancrea
46	chr4:74472200-74472600	Enhancers	Primary hematopoietic stem cells	blood
47	chr4:74472200-74472600	Active TSS	Colonic Mucosa	Colon
48	chr4:74472200-74472600	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr4:74472200-74472800	Enhancers	A549	lung
50	chr4:74472200-74473600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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