Variant report

Variant	rs1880177
Chromosome Location	chr6:69589956-69589957
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	chr6:69589839..69591611-chr6:69597828..69600787,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10485432	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12196150	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12524100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524957	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525831	1.00[CHB][hapmap]
rs12526204	0.89[ASN][1000 genomes]
rs12527569	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527597	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs12528028	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12528300	1.00[ASN][1000 genomes]
rs12528362	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12529646	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12530394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17399055	1.00[CHB][hapmap]
rs17476598	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs34580444	1.00[ASN][1000 genomes]
rs34629272	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3798984	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs4706035	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4706062	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4706744	1.00[CHB][hapmap]
rs62416367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416368	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416398	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416399	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416400	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416406	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62416440	1.00[ASN][1000 genomes]
rs62416449	1.00[ASN][1000 genomes]
rs62418264	1.00[ASN][1000 genomes]
rs62418267	1.00[ASN][1000 genomes]
rs62418268	1.00[ASN][1000 genomes]
rs62418270	1.00[ASN][1000 genomes]
rs62418272	1.00[ASN][1000 genomes]
rs62418273	1.00[ASN][1000 genomes]
rs62418276	1.00[ASN][1000 genomes]
rs62418565	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62418566	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62418567	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62418568	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62418570	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62418572	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62418577	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67653429	1.00[ASN][1000 genomes]
rs6921402	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73480159	1.00[ASN][1000 genomes]
rs7454736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748808	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs7759377	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs7767423	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]

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	nsv886132	chr6:69487204-69610281	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv886133	chr6:69549897-69610281	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1025548	chr6:69555181-69589956	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv886134	chr6:69571053-69605682	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv886135	chr6:69571053-69606748	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv528106	chr6:69581991-69610281	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv470831	chr6:69581991-69654650	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1880177	LMBRD1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69586600-69591200	Weak transcription	Brain Angular Gyrus	brain
2	chr6:69589000-69590000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:69589400-69590600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr6:69589600-69590400	Enhancers	Brain Substantia Nigra	brain
5	chr6:69589600-69590600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:69589600-69590800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:69589800-69591800	Enhancers	Brain Cingulate Gyrus	brain
8	chr6:69589800-69592800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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