Variant report

Variant	rs1564808
Chromosome Location	chr8:9962645-9962646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9954771..9956774-chr8:9960148..9962685,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10104911	0.82[CHB][hapmap]
rs10107485	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs11249969	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs11249970	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1160369	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11774411	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11783851	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11785434	0.94[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11785454	0.83[ASN][1000 genomes]
rs12542030	0.87[CEU][hapmap];0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs12545469	0.81[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs12545775	0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12545788	0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12545826	0.81[CHB][hapmap]
rs12547884	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12549943	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12550244	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs12550614	0.83[EUR][1000 genomes]
rs12674871	0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12679328	0.85[CHB][hapmap]
rs12680389	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs13249013	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.81[ASN][1000 genomes]
rs13250499	0.91[CEU][hapmap];0.80[CHB][hapmap];0.82[EUR][1000 genomes]
rs13256357	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs13261836	0.91[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs13279619	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1466555	0.84[ASN][1000 genomes]
rs1484645	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs17149332	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs17151142	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17151190	0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs17151201	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs17155393	0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1984863	0.81[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1994223	0.82[CHB][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs1994224	0.82[CHB][hapmap]
rs2016221	0.86[ASN][1000 genomes]
rs2046398	0.86[CHB][hapmap]
rs2409632	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2898242	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3735823	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs4294187	0.91[CHB][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs4840462	0.85[CHB][hapmap]
rs4840463	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4841277	0.84[EUR][1000 genomes]
rs4841279	0.95[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4841280	0.82[CHB][hapmap]
rs4841283	0.84[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs62488697	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62488698	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs625218	0.86[CHB][hapmap]
rs66602888	0.82[ASN][1000 genomes]
rs685218	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs6981546	0.86[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6983566	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6985791	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs6997865	0.85[CHB][hapmap]
rs7008407	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7008695	0.85[ASN][1000 genomes]
rs7012221	0.86[CEU][hapmap];0.80[CHB][hapmap];0.82[EUR][1000 genomes]
rs7012601	0.90[ASN][1000 genomes]
rs7016690	0.90[ASN][1000 genomes]
rs72626643	0.82[ASN][1000 genomes]
rs7830843	0.91[ASN][1000 genomes]
rs7831989	0.83[EUR][1000 genomes]
rs7832431	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7843390	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7843906	0.82[CHB][hapmap]
rs814421	0.81[MEX][hapmap]
rs814422	0.81[MEX][hapmap]
rs9329215	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs936749	0.81[CHB][hapmap]
rs963593	0.85[CHB][hapmap]
rs9644681	0.81[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	nsv1034343	chr8:9948342-10014155	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1564808	LONRF1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9957000-9965400	Weak transcription	Brain Angular Gyrus	brain
2	chr8:9958000-9963200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr8:9958000-9963200	Weak transcription	Gastric	stomach
4	chr8:9958600-9965200	Weak transcription	Fetal Heart	heart
5	chr8:9959800-9974000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr8:9961200-9967400	Weak transcription	Primary T cells from cord blood	blood
7	chr8:9961400-9970400	Weak transcription	Pancreas	Pancrea
8	chr8:9962000-9969000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr8:9962400-9963800	Weak transcription	Fetal Brain Male	brain
10	chr8:9962400-9964000	Enhancers	Fetal Brain Female	brain
11	chr8:9962400-9965800	Weak transcription	Psoas Muscle	Psoas
12	chr8:9962600-9966800	Weak transcription	Spleen	Spleen

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