Variant report

Variant	rs16889907
Chromosome Location	chr5:58785305-58785306
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	chr5:58784059..58785575-chr5:58790965..58792487,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10514861	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10514862	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10805515	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs11746896	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13180690	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs16889908	1.00[ASN][1000 genomes]
rs16889919	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16889920	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16889921	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs17796734	1.00[JPT][hapmap]
rs28435556	1.00[ASN][1000 genomes]
rs35987304	0.90[ASN][1000 genomes]
rs6450520	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6450521	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs66605058	1.00[ASN][1000 genomes]
rs66741919	0.80[AFR][1000 genomes]
rs67306207	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6885378	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7700365	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7706227	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7707043	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7717802	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7717819	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7717821	0.87[ASN][1000 genomes]

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	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58780800-58785400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:58783200-58785400	Weak transcription	Brain Germinal Matrix	brain
3	chr5:58783600-58785400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:58783800-58785800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:58783800-58787800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:58784000-58785400	Weak transcription	HSMMtube	muscle
7	chr5:58784000-58791600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:58784000-58792200	Weak transcription	Psoas Muscle	Psoas
9	chr5:58784000-58793200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:58784400-58787800	Weak transcription	Stomach Mucosa	stomach
11	chr5:58784400-58788400	Enhancers	A549	lung
12	chr5:58784600-58787000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:58784600-58791000	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:58784600-58797000	Weak transcription	Fetal Lung	lung
15	chr5:58784800-58790000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:58785200-58785400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr5:58785200-58785400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr5:58785200-58785400	Enhancers	Brain Cingulate Gyrus	brain
19	chr5:58785200-58785400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:58785200-58785400	Enhancers	Brain Substantia Nigra	brain
21	chr5:58785200-58785600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:58785200-58785800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr5:58785200-58785800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:58785200-58785800	Enhancers	Brain Hippocampus Middle	brain

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