Variant report

Variant	rs10498779
Chromosome Location	chr6:49801612-49801613
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49800763..49803553-chr6:49806581..49809390,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1053497	0.99[EUR][1000 genomes]
rs12191200	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12191354	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12191473	0.99[EUR][1000 genomes]
rs12193465	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12193606	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12196205	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12197213	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs12198253	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12198437	1.00[CEU][hapmap]
rs12198652	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12200231	0.99[EUR][1000 genomes]
rs12200365	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12200699	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12204651	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12204917	0.99[EUR][1000 genomes]
rs12207300	1.00[CEU][hapmap]
rs12209344	0.99[EUR][1000 genomes]
rs12209643	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12209658	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12211256	1.00[CEU][hapmap]
rs12211947	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12212140	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12213240	0.96[EUR][1000 genomes]
rs12213547	0.99[EUR][1000 genomes]
rs12216442	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12216534	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1572882	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs16879837	0.90[AFR][1000 genomes]
rs17663881	0.99[EUR][1000 genomes]
rs17663956	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1934854	1.00[CEU][hapmap]
rs3209304	0.99[EUR][1000 genomes]
rs45595734	0.95[EUR][1000 genomes]
rs56118419	0.99[EUR][1000 genomes]
rs57789146	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs593009	0.85[CEU][hapmap]
rs62404901	0.99[EUR][1000 genomes]
rs62404902	0.99[EUR][1000 genomes]
rs62404904	0.99[EUR][1000 genomes]
rs62404905	0.99[EUR][1000 genomes]
rs62404906	0.99[EUR][1000 genomes]
rs62404907	0.99[EUR][1000 genomes]
rs62404910	0.99[EUR][1000 genomes]
rs62404911	0.98[EUR][1000 genomes]
rs62404912	0.96[EUR][1000 genomes]
rs62404913	0.99[EUR][1000 genomes]
rs62404914	0.99[EUR][1000 genomes]
rs62404915	0.98[EUR][1000 genomes]
rs62404939	0.99[EUR][1000 genomes]
rs62404940	0.99[EUR][1000 genomes]
rs6908197	1.00[CEU][hapmap]
rs6928271	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7738293	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7751850	0.99[EUR][1000 genomes]
rs7757933	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7767534	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs9473668	1.00[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	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10498779	GPR115	cis	cerebellum	SCAN
rs10498779	TMEM14A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49800400-49801800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr6:49800400-49802000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr6:49800400-49802400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr6:49800600-49802400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr6:49801000-49802800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:49801400-49801800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr6:49801400-49803400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:49801600-49809400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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