Variant report

Variant	rs7769826
Chromosome Location	chr6:62871909-62871910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1007419	0.90[EUR][1000 genomes]
rs10223780	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10455666	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10806583	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1328890	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1401352	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1518908	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1518909	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1518911	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1518912	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1518916	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1610006	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1974087	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049007	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2176609	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3842920	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3842921	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3842922	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3846820	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3846821	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3846822	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3904141	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3904142	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3914604	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4487565	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4710674	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6455255	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902086	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912667	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6915599	0.87[EUR][1000 genomes]
rs6921170	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922243	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6929099	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6939991	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs765219	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7743234	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7744422	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7750316	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7758662	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9342665	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9346035	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9346109	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9346193	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9346218	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9351718	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9354733	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9354767	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9354781	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9354861	0.90[EUR][1000 genomes]
rs9363771	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9363792	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9454508	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs989138	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033794	chr6:61886428-62877254	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1027650	chr6:61886428-62877393	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv462963	chr6:61963172-62899514	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv603266	chr6:61963172-62899514	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv603268	chr6:61963173-62899514	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv932029	chr6:61967253-62900503	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv916376	chr6:61967253-62927185	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv529782	chr6:61971892-62877253	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv1022364	chr6:62019939-62877193	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv538261	chr6:62019939-62877193	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	esv17049	chr6:62178788-62919415	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv603277	chr6:62183901-62899514	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv1032202	chr6:62236498-62907004	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv538262	chr6:62236498-62907004	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	nsv1025290	chr6:62236498-62913561	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv538263	chr6:62236498-62913561	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
17	nsv948986	chr6:62504369-62899427	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv533083	chr6:62531786-62877253	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv603316	chr6:62600980-62927514	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv538267	chr6:62787337-62913561	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7769826	KHDRBS2	cis	hippocampus	BrainEAC
rs7769826	KHDRBS2	cis	brain	BrainEAC
rs7769826	KHDRBS2	cis	thalamus	BrainEAC
rs7769826	KHDRBS2	cis	substantia nigra	BrainEAC
rs7769826	KHDRBS2	cis	frontal cortex	BrainEAC
rs7769826	KHDRBS2	cis	intralobular white matter	BrainEAC

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:62845800-62872000	Weak transcription	Primary B cells from cord blood	blood
2	chr6:62859000-62872200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:62866200-62888000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:62871400-62872800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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