Variant report

Variant	rs7762864
Chromosome Location	chr6:88236213-88236214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1051131	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1051148	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10755484	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193380	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13194003	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2207146	0.85[EUR][1000 genomes]
rs2268993	0.86[EUR][1000 genomes]
rs2268994	0.86[EUR][1000 genomes]
rs2273129	0.85[EUR][1000 genomes]
rs2284908	0.85[EUR][1000 genomes]
rs2300906	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300909	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2307379	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2325064	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2754247	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2754248	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2754260	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2754262	0.85[EUR][1000 genomes]
rs2787893	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2787921	0.86[EUR][1000 genomes]
rs2787924	0.85[EUR][1000 genomes]
rs2814712	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3757368	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3934838	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4334949	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4464759	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4498321	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4587138	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4587143	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4706294	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707373	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707374	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707376	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707377	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707379	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707382	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707383	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6454631	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6454632	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454636	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6454638	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454640	0.88[EUR][1000 genomes]
rs6454641	0.88[EUR][1000 genomes]
rs6906769	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908386	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6916732	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918909	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923230	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6923355	0.84[EUR][1000 genomes]
rs6928160	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930600	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6931069	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6940150	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7741825	0.83[ASN][1000 genomes]
rs7742965	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7746465	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7750207	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7754350	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7755167	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7756225	0.81[ASN][1000 genomes]
rs7757636	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757794	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7761814	0.84[EUR][1000 genomes]
rs7772561	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7773906	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444504	0.85[EUR][1000 genomes]
rs9444512	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444519	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9444522	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444524	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444525	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444526	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444530	0.82[ASN][1000 genomes]
rs9450704	0.84[EUR][1000 genomes]
rs9450712	0.85[EUR][1000 genomes]
rs9450723	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450726	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450732	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450733	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450738	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450739	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450744	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450752	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450755	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450762	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs985764	0.89[EUR][1000 genomes];0.89[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	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	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7762864	SLC35A1	cis	multi-tissue	Pritchard
rs7762864	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs7762864	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs7762864	C6orf166	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88194000-88249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:88207200-88242600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr6:88210200-88240600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr6:88211000-88241200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:88212000-88245200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:88214200-88244400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:88215800-88240800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:88217800-88295800	Weak transcription	Fetal Brain Male	brain
9	chr6:88219000-88249000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:88220000-88244200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:88221000-88240800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr6:88225000-88250800	Weak transcription	Stomach Mucosa	stomach
13	chr6:88227000-88250200	Weak transcription	Fetal Heart	heart
14	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
15	chr6:88228000-88236600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:88228400-88239400	Weak transcription	Fetal Brain Female	brain
17	chr6:88228400-88250200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:88228600-88239000	Weak transcription	Right Ventricle	heart
20	chr6:88228600-88239200	Weak transcription	A549	lung
21	chr6:88228600-88239600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:88228600-88239600	Weak transcription	Brain Germinal Matrix	brain
23	chr6:88228600-88244200	Weak transcription	Aorta	Aorta
24	chr6:88228600-88244400	Weak transcription	Fetal Stomach	stomach
25	chr6:88228600-88249800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:88228600-88254000	Weak transcription	Gastric	stomach
27	chr6:88228600-88262800	Weak transcription	Small Intestine	intestine
28	chr6:88228600-88271400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:88228600-88285200	Weak transcription	Spleen	Spleen
30	chr6:88228800-88239400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:88228800-88240000	Weak transcription	NHLF	lung
32	chr6:88228800-88244400	Weak transcription	Pancreas	Pancrea
33	chr6:88228800-88253800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:88228800-88269600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:88229000-88239800	Weak transcription	Thymus	Thymus
36	chr6:88229400-88248800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:88229400-88248800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:88229400-88249000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:88229400-88261600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:88229400-88271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr6:88229600-88239400	Weak transcription	Colonic Mucosa	Colon
42	chr6:88229600-88244000	Weak transcription	Hela-S3	cervix
43	chr6:88229600-88254000	Weak transcription	Brain Anterior Caudate	brain
44	chr6:88229600-88289000	Weak transcription	Lung	lung
45	chr6:88230000-88249200	Weak transcription	Fetal Lung	lung
46	chr6:88230000-88267000	Weak transcription	Brain Substantia Nigra	brain
47	chr6:88230200-88237600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:88230400-88271200	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:88230600-88239000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr6:88230600-88239000	Weak transcription	Placenta Amnion	Placenta Amnion

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