Variant report

Variant	rs6808142
Chromosome Location	chr3:46556835-46556836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11130092	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12486039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176861	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34622981	0.81[ASN][1000 genomes]
rs34924380	0.87[ASN][1000 genomes]
rs35303057	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682820	0.87[ASN][1000 genomes]
rs62247799	0.87[ASN][1000 genomes]
rs6772937	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6791703	0.85[CEU][hapmap]
rs6800163	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7374675	1.00[JPT][hapmap]
rs7430431	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9311391	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9810340	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv963257	chr3:46553551-46557829	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6808142	LRRC2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46541000-46557600	Weak transcription	Left Ventricle	heart
2	chr3:46541000-46580200	Weak transcription	Fetal Heart	heart
3	chr3:46541200-46562200	Weak transcription	Right Ventricle	heart
4	chr3:46544800-46599400	Weak transcription	Right Atrium	heart
5	chr3:46545600-46558000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:46545600-46559200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:46549200-46585400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:46549400-46579000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:46549600-46578600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:46553200-46558000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:46553200-46558000	Weak transcription	HSMMtube	muscle
12	chr3:46555000-46567800	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:46555400-46561800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:46555800-46557600	Weak transcription	K562	blood
15	chr3:46556200-46558000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:46556400-46591000	Weak transcription	Psoas Muscle	Psoas
17	chr3:46556800-46560800	Weak transcription	Ovary	ovary

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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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