Variant report

Variant	rs6997464
Chromosome Location	chr8:10043374-10043375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10085917	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10093457	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10097315	0.84[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs10104463	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10283047	0.83[EUR][1000 genomes]
rs11249972	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11249973	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11777161	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11783143	0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11786117	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs11786120	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11787363	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13257383	0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs13258839	0.82[ASN][1000 genomes]
rs1484648	0.85[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17151318	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs17748267	0.85[CEU][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs17748464	0.85[CEU][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs1905630	0.96[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs1905631	0.96[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1905633	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1905634	0.85[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2409623	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28380058	0.83[ASN][1000 genomes]
rs28448513	0.81[AMR][1000 genomes]
rs28701812	0.82[EUR][1000 genomes]
rs2898240	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4255142	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4448276	0.92[CEU][hapmap];0.83[MEX][hapmap]
rs59255182	0.83[ASN][1000 genomes]
rs60032918	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60999585	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6601420	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6981758	0.81[JPT][hapmap]
rs6982806	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6994636	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6996281	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7006628	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7011004	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7011281	0.96[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7011821	0.96[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7812517	0.84[GIH][hapmap];0.85[JPT][hapmap]
rs7820236	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7822181	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7829478	0.96[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7842065	0.86[EUR][1000 genomes]
rs7845503	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1027280	chr8:9958259-10058984	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1850829	chr8:9958321-10045451	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv890344	chr8:9995515-10060638	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1026335	chr8:10037279-10139782	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6997464	XKR5	cis	parietal	SCAN
rs6997464	MORN3	trans	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10039600-10043400	Weak transcription	Fetal Brain Male	brain
2	chr8:10040800-10043800	Weak transcription	Brain Germinal Matrix	brain
3	chr8:10042000-10043600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr8:10042800-10043400	Weak transcription	Aorta	Aorta
5	chr8:10042800-10049400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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