Variant report

Variant	rs1889338
Chromosome Location	chr9:96133283-96133284
allele	C/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	POLR2A	chr9:96133193-96133513	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:96133259-96133544	H1-hESC	embryonic stem cell:	n/a	n/a
3	SETDB1	chr9:96133249-96133522	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95895210..95897945-chr9:96130128..96133625,4	MCF-7	breast:

Variant related genes	Relation type
RNU6-829P	TF binding region
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10512224	0.82[EUR][1000 genomes]
rs10512226	0.86[EUR][1000 genomes]
rs10739946	0.82[EUR][1000 genomes]
rs10761208	0.91[YRI][hapmap]
rs1111776	0.87[YRI][hapmap]
rs12553275	0.86[EUR][1000 genomes]
rs12684392	0.91[YRI][hapmap]
rs1331588	0.86[EUR][1000 genomes]
rs16909211	0.82[EUR][1000 genomes]
rs1891970	0.92[YRI][hapmap]
rs1931369	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1931372	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2151714	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2169756	0.83[YRI][hapmap]
rs2184256	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2494781	0.82[EUR][1000 genomes]
rs2494782	0.84[EUR][1000 genomes]
rs28403269	0.86[EUR][1000 genomes]
rs28421070	0.91[AMR][1000 genomes]
rs2991376	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes]
rs2995993	0.91[AMR][1000 genomes]
rs2995999	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes]
rs3001453	1.00[CEU][hapmap]
rs4469524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4548243	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4573340	0.86[EUR][1000 genomes]
rs4743913	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs4743914	0.92[YRI][hapmap]
rs4743916	0.95[EUR][1000 genomes]
rs4743917	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4743920	0.95[EUR][1000 genomes]
rs4744214	0.92[YRI][hapmap]
rs4744229	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55702483	0.86[EUR][1000 genomes]
rs55812345	0.82[EUR][1000 genomes]
rs56375911	0.86[EUR][1000 genomes]
rs58790127	0.86[EUR][1000 genomes]
rs60212988	0.86[EUR][1000 genomes]
rs6479473	0.92[YRI][hapmap]
rs6479479	0.95[EUR][1000 genomes]
rs6479480	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7020195	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7025514	0.85[YRI][hapmap]
rs7025611	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs7031917	0.84[YRI][hapmap]
rs7042492	0.92[YRI][hapmap]
rs73651204	0.82[EUR][1000 genomes]
rs73651206	0.86[EUR][1000 genomes]
rs73651227	0.86[EUR][1000 genomes]
rs73651228	0.86[EUR][1000 genomes]
rs73651229	0.86[EUR][1000 genomes]
rs73651232	0.86[EUR][1000 genomes]
rs7853075	0.85[YRI][hapmap]
rs7854217	0.86[EUR][1000 genomes]
rs7854349	0.86[EUR][1000 genomes]
rs7861929	0.82[EUR][1000 genomes]
rs7866298	0.92[YRI][hapmap]
rs7867386	0.84[YRI][hapmap]
rs7872608	0.92[YRI][hapmap]
rs7874126	0.82[EUR][1000 genomes]
rs999326	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96133200-96134400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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