Variant report

Variant	rs1321080
Chromosome Location	chr6:45358323-45358324
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45344406..45349479-chr6:45352255..45358580,11	MCF-7	breast:
2	chr6:45357171..45359418-chr6:45385191..45386849,2	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10456122	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10456543	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10456549	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10456553	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10807321	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs10948213	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10948214	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10948220	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10948223	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10948226	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10948233	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963924	1.00[JPT][hapmap]
rs11964690	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11966878	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11968637	0.92[ASN][1000 genomes]
rs12191262	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12191566	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12191751	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12192267	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12192890	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12193030	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12194628	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12197755	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12199256	1.00[JPT][hapmap]
rs12199720	1.00[JPT][hapmap]
rs12199871	1.00[JPT][hapmap]
rs12201555	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs12201563	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201899	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs12203052	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12203466	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12205523	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs12206561	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12210230	0.86[CEU][hapmap];0.85[ASN][1000 genomes]
rs12211510	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211519	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12212745	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12216308	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12524323	1.00[JPT][hapmap]
rs1321078	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1321079	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17209678	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17209741	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs17209769	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs17209895	0.90[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs17288250	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17288257	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17288320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17288327	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs1852983	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852984	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064628	0.83[EUR][1000 genomes]
rs2093900	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2894641	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4267941	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4400216	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4443508	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4479922	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62400335	0.92[ASN][1000 genomes]
rs62400353	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6919813	0.89[CEU][hapmap]
rs6919873	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs6919998	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6920046	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6927213	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72862930	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1321080	SUPT3H	cis	parietal	SCAN
rs1321080	LOC100132354	cis	cerebellum	SCAN
rs1321080	SUPT3H	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45354200-45358600	Enhancers	Muscle Satellite Cultured Cells	--
2	chr6:45356200-45358400	Enhancers	Osteobl	bone
3	chr6:45356800-45382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:45357800-45359000	Weak transcription	Placenta	Placenta

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