Variant report

Variant	rs6698069
Chromosome Location	chr1:72439152-72439153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10493488	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10493490	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs10493491	0.83[ASN][1000 genomes]
rs10889940	0.81[ASN][1000 genomes]
rs11209871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209888	1.00[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs1155261	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12023418	0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12024501	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12029938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12033580	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12034458	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12035363	0.83[ASN][1000 genomes]
rs12035495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12040021	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042679	1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs12043636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12047003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12047266	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17091962	0.84[JPT][hapmap]
rs17091997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17092178	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs17092217	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1834526	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2162238	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56134836	0.83[ASN][1000 genomes]
rs59416074	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61767482	0.81[ASN][1000 genomes]
rs6659791	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6667732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678735	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6696193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7520086	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7528016	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7553008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8179360	0.81[ASN][1000 genomes]
rs9787171	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv999162	chr1:72319163-72477496	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv534995	chr1:72319163-72477496	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv428763	chr1:72353556-72499701	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1007073	chr1:72419858-72734657	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1354	chr1:72431164-72475522	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6698069	LRRC40	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72434000-72439400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:72435800-72439400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:72438000-72443600	Weak transcription	Fetal Heart	heart

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