Variant report

Variant	rs2990140
Chromosome Location	chr9:21365043-21365044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21348973..21351463-chr9:21362839..21365132,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120235	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10116540	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs10117202	0.94[EUR][1000 genomes]
rs10120117	0.91[EUR][1000 genomes]
rs10122881	0.91[EUR][1000 genomes]
rs10124167	0.91[EUR][1000 genomes]
rs10738591	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs10757199	0.83[CEU][hapmap]
rs10811497	0.91[CEU][hapmap]
rs10811514	0.81[EUR][1000 genomes]
rs10811527	0.91[EUR][1000 genomes]
rs10811529	0.92[EUR][1000 genomes]
rs10964878	0.91[CEU][hapmap]
rs10964884	0.83[CEU][hapmap]
rs10964885	0.84[CEU][hapmap]
rs10964896	0.84[CEU][hapmap]
rs10964918	0.82[EUR][1000 genomes]
rs10964920	0.84[CEU][hapmap]
rs10964928	0.83[EUR][1000 genomes]
rs10964930	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs10964932	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs10964933	0.83[EUR][1000 genomes]
rs10964934	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs10964943	0.88[EUR][1000 genomes]
rs10964952	0.91[EUR][1000 genomes]
rs10964957	0.91[CEU][hapmap];0.81[CHB][hapmap];0.90[EUR][1000 genomes]
rs10964959	0.91[EUR][1000 genomes]
rs10964961	0.91[EUR][1000 genomes]
rs1112783	0.91[EUR][1000 genomes]
rs12551190	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12553763	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12553910	0.88[EUR][1000 genomes]
rs12555631	0.84[CEU][hapmap]
rs1330312	0.91[EUR][1000 genomes]
rs1330314	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1411436	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1424854	0.91[CEU][hapmap]
rs1590897	0.91[EUR][1000 genomes]
rs1820313	0.84[CEU][hapmap]
rs1831391	0.83[CEU][hapmap]
rs1834247	0.84[CEU][hapmap]
rs1854700	0.84[CEU][hapmap]
rs1928854	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1928855	0.82[EUR][1000 genomes]
rs1928856	0.81[EUR][1000 genomes]
rs1952690	0.89[EUR][1000 genomes]
rs2015345	0.91[CEU][hapmap]
rs2098814	0.84[CEU][hapmap]
rs28437205	0.83[EUR][1000 genomes]
rs2939	0.91[CEU][hapmap]
rs2988573	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2988574	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2990141	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs3750479	0.91[CEU][hapmap]
rs3758236	0.91[CEU][hapmap]
rs3955236	0.84[CEU][hapmap]
rs4112794	0.83[EUR][1000 genomes]
rs4568686	0.91[EUR][1000 genomes]
rs4582643	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4628333	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4977682	0.91[CEU][hapmap]
rs4977684	0.84[CEU][hapmap]
rs4977714	0.89[EUR][1000 genomes]
rs57122438	0.83[EUR][1000 genomes]
rs57146220	0.83[EUR][1000 genomes]
rs57371737	0.95[EUR][1000 genomes]
rs583396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596180	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs597440	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs604762	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs612966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs614541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs617881	0.81[EUR][1000 genomes]
rs618507	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637700	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs637949	0.90[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs647167	0.81[EUR][1000 genomes]
rs653778	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs660675	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662831	0.81[EUR][1000 genomes]
rs667214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667635	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs674189	0.81[EUR][1000 genomes]
rs681680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7019617	0.90[CEU][hapmap]
rs7019739	0.84[CEU][hapmap]
rs7030705	0.84[CEU][hapmap]
rs7031048	1.00[CEU][hapmap]
rs7033839	0.91[CEU][hapmap]
rs7035639	0.84[CEU][hapmap]
rs7037147	0.91[CEU][hapmap]
rs7041635	0.83[CEU][hapmap]
rs7047811	0.90[CEU][hapmap]
rs73418252	0.82[EUR][1000 genomes]
rs768849	0.84[CEU][hapmap]
rs7848803	0.81[EUR][1000 genomes]
rs7849623	0.91[CEU][hapmap]
rs7849862	0.91[CEU][hapmap]
rs7854247	0.82[CEU][hapmap]
rs7866359	0.84[CEU][hapmap]
rs7866640	0.94[EUR][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	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
2	nsv892736	chr9:21327141-21391698	Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv892737	chr9:21352862-21408824	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2752289	chr9:21361957-21499624	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21360200-21367000	Weak transcription	GM12878-XiMat	blood
2	chr9:21364000-21366000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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