Variant report

Variant	rs107689
Chromosome Location	chr6:88069333-88069334
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs107690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1080595	0.82[EUR][1000 genomes]
rs1080596	0.82[EUR][1000 genomes]
rs1201409	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12176253	0.82[ASN][1000 genomes]
rs12190280	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12207825	0.88[EUR][1000 genomes]
rs12664578	0.82[EUR][1000 genomes]
rs173333	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1753154	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs183599	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925695	0.82[EUR][1000 genomes]
rs1980790	0.82[EUR][1000 genomes]
rs1980792	0.82[EUR][1000 genomes]
rs2025630	0.82[EUR][1000 genomes]
rs2031518	0.81[EUR][1000 genomes]
rs2147919	0.81[EUR][1000 genomes]
rs2147920	0.82[EUR][1000 genomes]
rs2147921	0.82[EUR][1000 genomes]
rs2182181	0.81[EUR][1000 genomes]
rs2240459	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs242267	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs242270	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs242278	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs242279	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs242280	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs242281	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs242283	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs242285	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs242286	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs242287	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2474349	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2985039	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs369674	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs373646	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs376633	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812130	0.82[ASN][1000 genomes]
rs3812132	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs381782	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3857485	0.86[EUR][1000 genomes]
rs3857488	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs390272	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3903920	0.83[EUR][1000 genomes]
rs3904088	0.83[EUR][1000 genomes]
rs395358	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4110984	0.83[EUR][1000 genomes]
rs4110985	0.83[EUR][1000 genomes]
rs445434	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs446851	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447077	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs448580	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs451089	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs451465	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs451829	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4605853	0.82[EUR][1000 genomes]
rs4706289	0.82[EUR][1000 genomes]
rs4707346	0.82[EUR][1000 genomes]
rs4707347	0.83[EUR][1000 genomes]
rs4707351	0.82[EUR][1000 genomes]
rs4707352	0.82[EUR][1000 genomes]
rs4707356	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4707357	0.82[ASN][1000 genomes]
rs4707358	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs499373	0.83[EUR][1000 genomes]
rs586771	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6454591	0.82[EUR][1000 genomes]
rs6454592	0.82[EUR][1000 genomes]
rs6454594	0.82[EUR][1000 genomes]
rs6454595	0.86[EUR][1000 genomes]
rs6454596	0.82[ASN][1000 genomes]
rs6454597	0.80[ASN][1000 genomes]
rs6454598	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6454599	0.81[ASN][1000 genomes]
rs6454600	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6899394	0.82[ASN][1000 genomes]
rs6903219	0.88[EUR][1000 genomes]
rs6904310	0.82[EUR][1000 genomes]
rs6909021	0.82[EUR][1000 genomes]
rs6909200	0.82[EUR][1000 genomes]
rs6913721	0.82[EUR][1000 genomes]
rs6914193	0.83[EUR][1000 genomes]
rs6916994	0.82[ASN][1000 genomes]
rs6917432	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6921007	0.82[ASN][1000 genomes]
rs6921504	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6921619	0.82[EUR][1000 genomes]
rs6925648	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6926831	0.85[EUR][1000 genomes]
rs6934603	0.82[ASN][1000 genomes]
rs6937874	0.82[ASN][1000 genomes]
rs6940544	0.82[ASN][1000 genomes]
rs7453986	0.82[ASN][1000 genomes]
rs7739034	0.82[EUR][1000 genomes]
rs7739726	0.82[EUR][1000 genomes]
rs7742478	0.82[EUR][1000 genomes]
rs7746545	0.88[EUR][1000 genomes]
rs7747129	0.86[EUR][1000 genomes]
rs7748191	0.81[EUR][1000 genomes]
rs7752485	0.83[EUR][1000 genomes]
rs7752882	0.83[EUR][1000 genomes]
rs7753030	0.82[ASN][1000 genomes]
rs7755244	0.86[EUR][1000 genomes]
rs7757827	0.80[EUR][1000 genomes]
rs7758618	0.86[EUR][1000 genomes]
rs7763365	0.82[EUR][1000 genomes]
rs7766324	0.82[EUR][1000 genomes]
rs7767449	0.82[EUR][1000 genomes]
rs7768575	0.82[EUR][1000 genomes]
rs7776407	0.82[EUR][1000 genomes]
rs910563	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9344690	0.82[EUR][1000 genomes]
rs9344693	0.85[EUR][1000 genomes]
rs9344696	0.82[ASN][1000 genomes]
rs9344697	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9351117	0.82[EUR][1000 genomes]
rs9351124	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9353462	0.82[EUR][1000 genomes]
rs9353463	0.82[EUR][1000 genomes]
rs9353464	0.83[EUR][1000 genomes]
rs9353465	0.86[EUR][1000 genomes]
rs9353468	0.80[ASN][1000 genomes]
rs9353473	0.82[ASN][1000 genomes]
rs9353483	0.88[EUR][1000 genomes]
rs9359743	0.82[ASN][1000 genomes]
rs9359748	0.88[EUR][1000 genomes]
rs9359749	0.80[EUR][1000 genomes]
rs9362408	0.82[EUR][1000 genomes]
rs9362415	0.80[ASN][1000 genomes]
rs9362417	0.81[ASN][1000 genomes]
rs9362427	0.87[EUR][1000 genomes]
rs9450634	0.81[EUR][1000 genomes]
rs9450647	0.82[ASN][1000 genomes]
rs9450650	0.82[ASN][1000 genomes]
rs9450652	0.82[ASN][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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs107689	C6orf164	cis	Esophagus Muscularis	GTEx
rs107689	SLC35A1	cis	multi-tissue	Pritchard
rs107689	C6orf164	cis	Artery Tibial	GTEx
rs107689	C6orf164	cis	lung	GTEx
rs107689	C6orf164	cis	Thyroid	GTEx
rs107689	C6orf164	cis	Whole Blood	GTEx
rs107689	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs107689	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs107689	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs107689	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88039000-88078400	Weak transcription	Fetal Stomach	stomach
2	chr6:88040200-88075800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:88044000-88071400	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:88044400-88076000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:88044800-88072600	Weak transcription	Adipose Nuclei	Adipose
7	chr6:88044800-88075600	Weak transcription	Fetal Lung	lung
8	chr6:88051200-88071200	Weak transcription	Ovary	ovary
9	chr6:88051600-88070000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:88054800-88075600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
12	chr6:88055000-88075800	Weak transcription	Primary B cells from cord blood	blood
13	chr6:88055200-88072800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:88057400-88073800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:88057600-88077200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:88061400-88070400	Weak transcription	Right Ventricle	heart
17	chr6:88061600-88094600	Weak transcription	Left Ventricle	heart
18	chr6:88062800-88070800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:88063400-88075800	Weak transcription	Aorta	Aorta
20	chr6:88067200-88069800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:88067800-88071800	Weak transcription	Fetal Intestine Small	intestine
22	chr6:88068400-88069800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr6:88068800-88075800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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