Variant report

Variant	rs251489
Chromosome Location	chr3:142699541-142699542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000268129	Chromatin interaction
ENSG00000241570	Chromatin interaction
ENSG00000188582	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs185182	0.84[ASN][1000 genomes]
rs251484	1.00[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs251485	0.81[EUR][1000 genomes]
rs251486	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs251487	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs251490	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs251491	0.83[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs251492	0.84[ASN][1000 genomes]
rs3101060	1.00[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36284	0.84[ASN][1000 genomes]
rs36285	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs40160	0.95[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs668856	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs251489	U2SURP	cis	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142694200-142699800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:142695400-142700200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:142695800-142700200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:142695800-142701000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:142695800-142701000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:142695800-142701400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:142695800-142705800	Weak transcription	Left Ventricle	heart
8	chr3:142696000-142705800	Weak transcription	Right Atrium	heart
9	chr3:142696200-142700000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:142696400-142699600	Weak transcription	HepG2	liver
11	chr3:142696400-142700200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:142698400-142699800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:142698600-142700800	Enhancers	K562	blood
14	chr3:142699000-142701600	Enhancers	A549	lung
15	chr3:142699200-142700200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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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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