Variant report

Variant	rs700002
Chromosome Location	chr6:49786893-49786894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:49780866..49783240-chr6:49785273..49787244,2	K562	blood:
2	chr6:49780840..49782366-chr6:49785273..49786896,2	K562	blood:
3	chr6:49785264..49787289-chr6:49788003..49790525,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf141-1	chr6:49786838-49787037	ENSG00000235122.2
2	lnc-C6orf141-1	chr6:49786838-49787037	NONHSAT113065
3	lnc-C6orf141-1	chr6:49786836-49787035	ENSG00000235122.3

No data

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1053497	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12191200	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs12191354	1.00[AFR][1000 genomes]
rs12191473	1.00[AFR][1000 genomes]
rs12193465	1.00[AFR][1000 genomes]
rs12193606	1.00[AFR][1000 genomes]
rs12194388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12194551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12195902	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12196205	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs12198253	1.00[AFR][1000 genomes]
rs12198437	0.86[CEU][hapmap]
rs12198652	1.00[AFR][1000 genomes]
rs12200231	1.00[AFR][1000 genomes]
rs12200365	1.00[AFR][1000 genomes]
rs12200699	1.00[AFR][1000 genomes]
rs12204651	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs12204917	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12207762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12209344	1.00[AFR][1000 genomes]
rs12209643	1.00[AFR][1000 genomes]
rs12209658	1.00[AFR][1000 genomes]
rs12211947	1.00[AFR][1000 genomes]
rs12212140	1.00[AFR][1000 genomes]
rs12213240	1.00[AFR][1000 genomes]
rs12213547	1.00[AFR][1000 genomes]
rs12216442	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12216534	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1572882	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs17663881	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17663956	1.00[AFR][1000 genomes]
rs3209304	1.00[AFR][1000 genomes]
rs45595734	1.00[AFR][1000 genomes]
rs493206	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55824128	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56118419	1.00[AFR][1000 genomes]
rs587310	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs593009	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609103	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs609927	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404901	1.00[AFR][1000 genomes]
rs62404902	1.00[AFR][1000 genomes]
rs62404905	1.00[AFR][1000 genomes]
rs62404906	1.00[AFR][1000 genomes]
rs62404907	1.00[AFR][1000 genomes]
rs62404910	1.00[AFR][1000 genomes]
rs62404911	1.00[AFR][1000 genomes]
rs62404912	1.00[AFR][1000 genomes]
rs62404913	1.00[AFR][1000 genomes]
rs62404914	1.00[AFR][1000 genomes]
rs62404915	1.00[AFR][1000 genomes]
rs62404939	1.00[AFR][1000 genomes]
rs62404940	1.00[AFR][1000 genomes]
rs684749	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686522	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928271	1.00[AFR][1000 genomes]
rs7738293	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs780443	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473667	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3434423	chr6:49771042-49788886	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs700002	GPR115	cis	cerebellum	SCAN
rs700002	GCM1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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