Variant report

Variant	rs251491
Chromosome Location	chr3:142698748-142698749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10790	0.82[CEU][hapmap]
rs185182	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290549	0.82[CEU][hapmap]
rs251484	0.83[ASW][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs251485	0.90[EUR][1000 genomes]
rs251486	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs251487	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs251489	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]
rs251490	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs251492	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3101060	0.83[ASW][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs36284	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36285	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40160	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs42381	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs668856	0.88[ASN][1000 genomes]
rs7652745	0.82[CEU][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs251491	SR140	Cis_1M	lymphoblastoid	RTeQTL
rs251491	U2SURP	cis	lymphoblastoid	seeQTL
rs251491	SLC9A9	cis	parietal	SCAN

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	chr3:142696400-142699200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:142696400-142699600	Weak transcription	HepG2	liver
12	chr3:142696400-142700200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:142698400-142699800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:142698600-142699000	Weak transcription	A549	lung
15	chr3:142698600-142700800	Enhancers	K562	blood

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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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