Variant report

Variant	rs717822
Chromosome Location	chr6:164405785-164405786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10484512	0.88[AFR][1000 genomes]
rs10484513	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10484515	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10945939	0.81[ASN][1000 genomes]
rs10945940	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10945941	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10945942	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10945944	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10945945	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12191111	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545107	0.81[ASN][1000 genomes]
rs16895846	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1756	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34021940	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34091550	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34413611	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34561573	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34727935	0.80[ASN][1000 genomes]
rs34994154	0.88[ASN][1000 genomes]
rs35668088	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4499903	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709030	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709031	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709799	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4709800	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4709802	0.90[ASN][1000 genomes]
rs4709803	0.87[ASN][1000 genomes]
rs4709804	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473823	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs491901	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs551475	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs616299	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs617616	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62435513	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62435541	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs634032	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs656371	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680187	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7451221	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751193	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356176	0.90[ASN][1000 genomes]
rs9364711	0.82[EUR][1000 genomes];0.85[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	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1026707	chr6:164188210-164749206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv538527	chr6:164188210-164749206	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830858	chr6:164296054-164455743	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs717822	MAP3K4	cis	cerebellum	SCAN
rs717822	CNO	trans	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164393800-164413800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:164404600-164405800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:164404600-164405800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr6:164404800-164406400	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:164404800-164406400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:164404800-164406600	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:164404800-164406800	Weak transcription	Ovary	ovary
8	chr6:164404800-164407000	Weak transcription	Left Ventricle	heart
9	chr6:164404800-164407000	Weak transcription	Right Atrium	heart
10	chr6:164405000-164405800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:164405000-164406200	Enhancers	GM12878-XiMat	blood
12	chr6:164405000-164406400	Enhancers	Fetal Brain Male	brain
13	chr6:164405000-164407000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:164405000-164407000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:164405000-164407400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:164405200-164405800	Enhancers	Primary B cells from cord blood	blood
17	chr6:164405200-164405800	Enhancers	Brain Anterior Caudate	brain
18	chr6:164405200-164405800	Enhancers	Brain Substantia Nigra	brain
19	chr6:164405200-164406000	Enhancers	Brain Germinal Matrix	brain
20	chr6:164405200-164406000	Enhancers	Brain Hippocampus Middle	brain
21	chr6:164405200-164406200	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr6:164405200-164406800	Enhancers	NH-A	brain
23	chr6:164405200-164407000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:164405400-164405800	Enhancers	Fetal Thymus	thymus
25	chr6:164405400-164406000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:164405400-164406200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:164405400-164406600	Weak transcription	Fetal Brain Female	brain
28	chr6:164405600-164405800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:164405600-164406000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:164405600-164406000	Enhancers	HSMMtube	muscle
31	chr6:164405600-164406200	Weak transcription	Pancreas	Pancrea
32	chr6:164405600-164406800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:164405600-164407800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:164405600-164409600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:164405600-164412800	Weak transcription	Brain Cingulate Gyrus	brain

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