Variant report

Variant	rs6695609
Chromosome Location	chr1:166953866-166953867
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:166953793-166953960	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:166945300..166947626-chr1:166953556..166955132,2	K562	blood:
2	chr1:166953493..166955548-chr1:167027824..167030715,2	K562	blood:

Variant related genes	Relation type
MAEL	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1041238	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10918599	0.87[AMR][1000 genomes]
rs10918600	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs10918603	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10918607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs10918608	0.86[ASN][1000 genomes]
rs11578336	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs11579987	0.88[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs11802666	0.87[ASN][1000 genomes]
rs11805946	0.88[ASN][1000 genomes]
rs12118335	0.81[ASN][1000 genomes]
rs12126991	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12131832	0.85[ASN][1000 genomes]
rs12133327	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12134016	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12564877	0.86[ASN][1000 genomes]
rs12569084	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2072742	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2142615	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs2235184	0.82[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap]
rs2296837	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2312487	0.86[ASN][1000 genomes]
rs2312675	0.80[CHB][hapmap];0.83[AMR][1000 genomes]
rs3736988	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs41269702	1.00[ASN][1000 genomes]
rs56093705	0.81[ASN][1000 genomes]
rs61447801	0.88[ASN][1000 genomes]
rs61606407	1.00[ASN][1000 genomes]
rs61815130	0.87[AMR][1000 genomes]
rs61815132	0.86[AMR][1000 genomes]
rs6427047	0.82[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes]
rs6427053	0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs6655947	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6660048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs6662130	0.88[ASN][1000 genomes]
rs6665341	1.00[ASN][1000 genomes]
rs6669886	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs6673622	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6673720	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6681562	0.85[ASN][1000 genomes]
rs6681571	0.84[ASN][1000 genomes]
rs6682062	1.00[ASN][1000 genomes]
rs6695162	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6696203	0.88[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6697417	0.90[ASN][1000 genomes]
rs6699159	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs742048	0.88[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes]
rs7511933	0.88[ASN][1000 genomes]
rs7518155	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7528849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7533688	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7545806	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7545911	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7550698	1.00[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	nsv1004148	chr1:166951869-167016311	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2750815	chr1:166953866-167180342	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6695609	FAM78B	cis	parietal	SCAN
rs6695609	C1orf110	cis	parietal	SCAN
rs6695609	RGS4	cis	parietal	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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