Variant report

Variant	rs761541
Chromosome Location	chr6:144216973-144216974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12526647	1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12527533	1.00[JPT][hapmap]
rs12527718	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12527740	0.82[CHB][hapmap];1.00[CHD][hapmap];0.96[ASN][1000 genomes]
rs35274932	0.96[ASN][1000 genomes]
rs4140441	0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs4895623	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs4896683	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4896684	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs4896685	0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs4896686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570586	1.00[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap]
rs761540	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764667	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7742707	1.00[CHB][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7755147	0.82[CHB][hapmap]
rs9484827	0.88[CHD][hapmap]
rs9496799	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3522138	chr6:144174685-144367463	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3522139	chr6:144174685-144367463	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830830	chr6:144177942-144380870	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs761541	LTV1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144186000-144223000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:144204800-144220800	Weak transcription	Primary B cells from cord blood	blood
3	chr6:144205800-144222600	Weak transcription	Fetal Stomach	stomach
4	chr6:144206000-144217400	Weak transcription	Fetal Lung	lung
5	chr6:144207200-144222800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:144216200-144217200	Weak transcription	GM12878-XiMat	blood
7	chr6:144216400-144218200	Enhancers	Fetal Muscle Leg	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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