Variant report

Variant	rs1458999
Chromosome Location	chr8:113878100-113878101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:185653287..185655288-chr8:113877614..113879705,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136527	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1026488	0.81[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1026489	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11787239	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11986076	0.87[ASN][1000 genomes]
rs13256271	0.84[ASN][1000 genomes]
rs13256724	1.00[JPT][hapmap]
rs13259225	1.00[JPT][hapmap]
rs13259298	0.87[ASN][1000 genomes]
rs13261160	0.87[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs13261301	1.00[JPT][hapmap]
rs13264919	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13266975	0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs13267779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13272429	1.00[JPT][hapmap]
rs13275178	1.00[JPT][hapmap]
rs13275398	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs13276278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1350566	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1350567	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1380134	0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1380136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1380139	0.98[ASN][1000 genomes]
rs1380140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1380141	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1458994	1.00[JPT][hapmap]
rs1459000	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1459006	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1459007	0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs16884158	0.80[YRI][hapmap]
rs170760	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1813415	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947633	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1979305	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1993607	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045540	0.98[ASN][1000 genomes]
rs2125552	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2125553	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2194601	1.00[JPT][hapmap]
rs2216891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2219486	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs231278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs231280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs231282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs231283	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs231284	0.84[ASN][1000 genomes]
rs231287	0.84[ASN][1000 genomes]
rs231288	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs231301	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs231302	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs231305	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs231306	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs231312	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs231313	0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs231314	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs231315	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs231317	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs231320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs231321	0.87[ASN][1000 genomes]
rs231322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[ASN][1000 genomes]
rs231323	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2446469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2511523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2511524	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511527	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2511529	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511530	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511535	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28830583	0.87[ASN][1000 genomes]
rs370168	1.00[CHB][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs373880	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs3950980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4028265	0.98[ASN][1000 genomes]
rs4876298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4876499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4876501	0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7009209	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7013313	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs7818598	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs958815	0.85[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2753595	chr8:113283214-114190390	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv534270	chr8:113585830-113979075	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
3	esv2754315	chr8:113736824-114048824	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv891326	chr8:113777669-114091732	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv891327	chr8:113828980-114109342	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1458999	NUDCD1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:113877200-113878400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr8:113878000-113878400	Enhancers	HUES48 Cell Line	embryonic stem cell

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