Variant report

Variant	rs10002880
Chromosome Location	chr4:174069718-174069719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGB2-10	chr4:174069310-174069814	NONHSAT099221

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10010943	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018520	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520255	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs11932721	1.00[CHB][hapmap]
rs11942280	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[MEX][hapmap]
rs13137793	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13151627	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs1316412	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17059191	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17059255	1.00[CHB][hapmap]
rs2006808	0.95[EUR][1000 genomes]
rs2332653	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34303112	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35773919	0.95[EUR][1000 genomes]
rs35932490	0.95[EUR][1000 genomes]
rs62341090	0.95[EUR][1000 genomes]
rs62341092	0.95[EUR][1000 genomes]
rs6553687	1.00[CHB][hapmap]
rs6822924	0.81[CEU][hapmap]
rs6829566	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs6835517	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs6840087	1.00[CHB][hapmap]
rs6840841	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855544	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856630	1.00[CHB][hapmap]
rs71609812	0.95[EUR][1000 genomes]
rs722826	0.81[CEU][hapmap]
rs722827	0.81[CEU][hapmap]
rs7664269	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664652	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669267	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689627	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7689781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312537	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312538	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs934358	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs9884450	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884453	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884604	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10002880	SCRG1	cis	parietal	SCAN
rs10002880	SCRG1	cis	cerebellum	SCAN
rs10002880	GALNT7	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174047000-174079000	Weak transcription	Fetal Thymus	thymus
2	chr4:174055000-174086000	Weak transcription	Thymus	Thymus
3	chr4:174065200-174087200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:174065400-174083600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:174066800-174089000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:174066800-174089000	Weak transcription	HSMM	muscle
7	chr4:174069200-174069800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:174069200-174088800	Weak transcription	HMEC	breast

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