Variant report

Variant	rs17288390
Chromosome Location	chr6:45384018-45384019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:41400879..41402620-chr6:45382949..45384449,2	MCF-7	breast:
2	chr6:45381884..45384461-chr6:45385432..45387065,2	MCF-7	breast:
3	chr6:45346856..45348655-chr6:45382726..45385574,2	K562	blood:
4	chr6:45381712..45384428-chr6:45387465..45389865,2	MCF-7	breast:
5	chr6:45345681..45347197-chr6:45381853..45384436,2	MCF-7	breast:
6	chr6:45383474..45385302-chr6:45402445..45404641,2	K562	blood:

Variant related genes	Relation type
ENSG00000271857	Chromatin interaction
ENSG00000124813	Chromatin interaction
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1004130	0.83[ASN][1000 genomes]
rs10948234	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11498195	0.83[ASN][1000 genomes]
rs1575060	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17209846	0.81[JPT][hapmap]
rs17209853	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs17209874	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs17209881	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs17288355	0.81[JPT][hapmap]
rs17288397	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1977152	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1997995	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2819855	0.81[CEU][hapmap]
rs3749864	0.83[ASN][1000 genomes]
rs3792952	0.83[ASN][1000 genomes]
rs3805811	0.83[ASN][1000 genomes]
rs3805818	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3828722	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3828723	0.83[ASN][1000 genomes]
rs4370348	0.83[ASN][1000 genomes]
rs4413613	0.83[ASN][1000 genomes]
rs4413614	0.83[ASN][1000 genomes]
rs59397804	0.83[ASN][1000 genomes]
rs6921145	0.83[ASN][1000 genomes]
rs72862937	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7749637	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7751427	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7768466	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7768666	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7770471	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7771980	0.83[ASN][1000 genomes]
rs9296459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45377200-45386400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:45382800-45386800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:45383000-45384200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:45383000-45386200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:45383000-45387000	Enhancers	Osteobl	bone
6	chr6:45383200-45384800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:45383200-45385400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:45383200-45386800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:45383400-45384400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:45383400-45384400	Enhancers	GM12878-XiMat	blood
11	chr6:45383400-45385000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:45383400-45385200	Enhancers	NHDF-Ad	bronchial
13	chr6:45383400-45386800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:45383400-45387200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:45383400-45387200	Weak transcription	Spleen	Spleen
16	chr6:45383400-45387400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:45383600-45384800	Enhancers	Hela-S3	cervix
18	chr6:45383600-45384800	Enhancers	NHLF	lung
19	chr6:45383600-45386000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr6:45383600-45386800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:45383600-45387000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:45383800-45385400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr6:45383800-45387000	Weak transcription	NHEK	skin
24	chr6:45384000-45384200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:45384000-45384200	Enhancers	NH-A	brain
26	chr6:45384000-45384800	Enhancers	HSMM	muscle

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