Variant report

Variant	rs7545932
Chromosome Location	chr1:211002077-211002078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10863864	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10863865	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11119614	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119620	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11119625	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11119626	0.91[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11485201	0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11580309	0.92[ASN][1000 genomes]
rs12058816	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12059106	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12059948	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12065074	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12069980	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12078503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085875	0.81[ASN][1000 genomes]
rs12092880	0.97[ASN][1000 genomes]
rs12094756	0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1343150	0.91[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17016986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1770219	0.81[JPT][hapmap]
rs2358094	0.92[ASN][1000 genomes]
rs28402221	0.96[ASN][1000 genomes]
rs55646513	0.86[ASN][1000 genomes]
rs56336842	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs58579065	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59197723	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6658580	0.86[JPT][hapmap]
rs6666042	0.86[JPT][hapmap]
rs6666924	0.84[ASN][1000 genomes]
rs6668151	0.83[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs67483865	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7515909	0.86[JPT][hapmap]
rs7546472	0.86[JPT][hapmap]
rs7553542	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs9730476	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832503	chr1:210948760-211103163	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7545932	CR1L	cis	cerebellum	SCAN
rs7545932	RAB7L1	cis	cerebellum	SCAN
rs7545932	NEK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210996600-211015000	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:210996800-211002600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:210997000-211002200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:211002000-211002600	Enhancers	HSMMtube	muscle
5	chr1:211002000-211003800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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