Variant report

Variant	rs4399689
Chromosome Location	chr2:174030566-174030567
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11680555	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11687539	0.97[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17710065	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17710437	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1809139	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2043950	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2358088	0.88[ASN][1000 genomes]
rs3754739	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769159	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769162	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769163	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769173	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4972532	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56980119	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59500540	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61264428	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62175824	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs722864	0.81[ASN][1000 genomes]
rs734993	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73974105	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs746179	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7567355	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7575319	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7601536	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs935006	0.91[ASN][1000 genomes]
rs935007	0.89[EUR][1000 genomes];0.91[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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv834461	chr2:173979734-174038471	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4399689	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174015400-174047000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:174016200-174048800	Weak transcription	K562	blood
3	chr2:174024800-174037200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:174026000-174030600	Weak transcription	Pancreas	Pancrea
5	chr2:174026000-174036800	Weak transcription	Small Intestine	intestine
6	chr2:174026000-174037400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:174026000-174037800	Weak transcription	Aorta	Aorta
8	chr2:174026000-174069000	Weak transcription	Primary B cells from cord blood	blood
9	chr2:174026200-174035200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:174026200-174036800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:174026200-174040600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:174026200-174045000	Weak transcription	Fetal Intestine Small	intestine
13	chr2:174026400-174030600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:174026400-174036600	Weak transcription	NHEK	skin
15	chr2:174026400-174039600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:174026400-174047600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:174026600-174030800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:174026600-174037800	Weak transcription	Right Ventricle	heart
19	chr2:174026600-174048800	Weak transcription	Liver	Liver
20	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
21	chr2:174027000-174032800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:174027200-174030800	Weak transcription	Fetal Intestine Large	intestine
23	chr2:174028200-174036600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:174028200-174044200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:174028400-174030600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:174028400-174036000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:174028400-174036600	Weak transcription	Adipose Nuclei	Adipose
28	chr2:174028400-174054600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:174028600-174033200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:174028800-174031000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:174029000-174030800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:174029000-174031000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:174029000-174031200	Enhancers	NHDF-Ad	bronchial
34	chr2:174029000-174032600	Enhancers	NHLF	lung
35	chr2:174029200-174032800	Enhancers	A549	lung
36	chr2:174030000-174031000	Enhancers	Ovary	ovary
37	chr2:174030000-174031000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr2:174030000-174037600	Weak transcription	Left Ventricle	heart
39	chr2:174030000-174052200	Weak transcription	Fetal Lung	lung
40	chr2:174030200-174031200	Enhancers	Colon Smooth Muscle	Colon
41	chr2:174030200-174032600	Enhancers	Hela-S3	cervix
42	chr2:174030400-174030600	Enhancers	Psoas Muscle	Psoas
43	chr2:174030400-174030800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:174030400-174030800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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