Variant report

Variant	rs6546319
Chromosome Location	chr2:67843200-67843201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10196304	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10490723	0.93[ASN][1000 genomes]
rs12477088	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618268	0.89[ASN][1000 genomes]
rs12986714	0.82[ASN][1000 genomes]
rs12987509	0.89[ASN][1000 genomes]
rs12989021	0.88[ASN][1000 genomes]
rs12992403	0.91[ASN][1000 genomes]
rs12993096	0.82[ASN][1000 genomes]
rs12997331	0.89[ASN][1000 genomes]
rs13003698	0.87[ASN][1000 genomes]
rs13005138	0.88[ASN][1000 genomes]
rs13013880	0.89[ASN][1000 genomes]
rs13019532	0.89[ASN][1000 genomes]
rs13021903	0.93[ASN][1000 genomes]
rs13023342	0.88[ASN][1000 genomes]
rs13025342	0.87[ASN][1000 genomes]
rs13025376	0.92[ASN][1000 genomes]
rs13028371	0.94[ASN][1000 genomes]
rs1430786	0.83[ASN][1000 genomes]
rs17033996	0.88[ASN][1000 genomes]
rs2861683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2861685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2861691	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34724856	0.85[ASN][1000 genomes]
rs35002785	0.89[ASN][1000 genomes]
rs35179846	0.89[ASN][1000 genomes]
rs35820615	0.89[ASN][1000 genomes]
rs4362542	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4465757	0.80[ASN][1000 genomes]
rs4542832	0.83[ASN][1000 genomes]
rs4671187	0.85[CHB][hapmap]
rs62156279	0.89[ASN][1000 genomes]
rs6546315	0.89[ASN][1000 genomes]
rs6731513	0.91[ASN][1000 genomes]
rs6732490	0.87[ASN][1000 genomes]
rs6746168	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6756226	0.87[ASN][1000 genomes]
rs6760893	0.89[ASN][1000 genomes]
rs980226	0.91[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	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6546319	PELI1	cis	cerebellum	SCAN
rs6546319	NFU1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67840200-67843600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:67840200-67847800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:67840400-67843200	Weak transcription	Right Atrium	heart
4	chr2:67842200-67844000	Weak transcription	NHDF-Ad	bronchial
5	chr2:67843000-67844600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:67843200-67844000	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:67843200-67844200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:67843200-67844200	Enhancers	Right Atrium	heart
9	chr2:67843200-67845000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:67843200-67845000	Enhancers	Stomach Smooth Muscle	stomach
11	chr2:67843200-67845400	Enhancers	Rectal Smooth Muscle	rectum

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