Variant report

Variant	rs4378206
Chromosome Location	chr1:152369913-152369914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:152369833-152370431	MCF-7	breast:	n/a	n/a
2	CTCF	chr1:152369900-152370050	GM06990	blood:	n/a	n/a
3	CTCF	chr1:152369889-152370474	MCF-7	breast:	n/a	n/a
4	CTCF	chr1:152369891-152370436	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:152369874..152370523-chr1:152423403..152423977,2	MCF-7	breast:
2	chr1:152369672..152370659-chr1:152413047..152413901,4	MCF-7	breast:
3	chr1:152368385..152370359-chr1:152413395..152416053,2	MCF-7	breast:
4	chr1:152369802..152370305-chr1:152430586..152431135,2	K562	blood:
5	chr1:152369903..152370605-chr1:152413321..152413987,3	MCF-7	breast:
6	chr1:152369716..152370381-chr10:53149139..53149795,2	MCF-7	breast:

No data

Variant related genes	Relation type
HMGN3P1	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10788835	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs10888486	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11204982	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11204985	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204986	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204987	0.84[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204995	0.80[ASN][1000 genomes]
rs11204996	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204997	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204998	0.80[ASN][1000 genomes]
rs11301808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11583558	0.83[AMR][1000 genomes]
rs11588022	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11590822	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11803108	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs12022217	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12024486	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12027445	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12029431	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12029633	0.80[AMR][1000 genomes]
rs12032854	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12049036	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12402680	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12403031	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12407319	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12408401	1.00[CEU][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12568784	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1858485	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1923493	0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1923505	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923506	0.81[ASN][1000 genomes]
rs1923509	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1933066	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2065954	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2146119	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs2282303	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2525	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3120665	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3120666	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3120667	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3126099	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3753443	0.81[JPT][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3753444	0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3818831	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3829868	0.81[JPT][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4285700	0.81[JPT][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs45541239	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587668	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6679449	0.93[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs6679899	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6693160	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs726863	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7514696	0.80[ASN][1000 genomes]
rs7515448	0.87[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7521839	0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs941935	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9633410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4378206	GABPB2	cis	cerebellum	SCAN
rs4378206	IVL	cis	parietal	SCAN
rs4378206	AQP10	cis	parietal	SCAN
rs4378206	SLC27A3	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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