Variant report

Variant	rs609707
Chromosome Location	chr1:67176983-67176984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67172247..67174334-chr1:67176397..67179152,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10493414	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10889648	0.95[ASN][1000 genomes]
rs11208949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11208950	0.91[ASN][1000 genomes]
rs12029896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12117649	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12563682	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1325265	0.94[ASN][1000 genomes]
rs1325266	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs1359462	0.95[ASN][1000 genomes]
rs1359463	0.91[ASN][1000 genomes]
rs2031477	0.93[ASN][1000 genomes]
rs2146905	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap]
rs2454325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4143025	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs473470	0.87[ASW][hapmap];0.90[YRI][hapmap]
rs475762	0.93[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs510771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553729	0.81[YRI][hapmap]
rs566057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650202	0.89[ASW][hapmap];1.00[YRI][hapmap]
rs665379	0.93[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6668681	0.95[ASN][1000 genomes]
rs6682534	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs6686476	0.85[ASN][1000 genomes]
rs678253	0.81[YRI][hapmap]
rs678499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs682896	1.00[YRI][hapmap]
rs693956	0.89[ASW][hapmap];0.81[YRI][hapmap]
rs7529763	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9988481	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv830093	chr1:67173594-67348264	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs609707	LRRC7	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67155800-67177200	Weak transcription	Brain Anterior Caudate	brain
2	chr1:67156000-67177200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
4	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
5	chr1:67157200-67189600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:67158200-67189400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:67158400-67191400	Weak transcription	Left Ventricle	heart
9	chr1:67158600-67189400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:67160400-67189400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:67165200-67191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:67165400-67187600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:67165400-67191600	Weak transcription	Aorta	Aorta
14	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
15	chr1:67168000-67185000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:67170200-67186800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:67171400-67189400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:67171400-67198000	Weak transcription	NHLF	lung

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