Variant report

Variant	rs12653924
Chromosome Location	chr5:89927354-89927355
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	chr5:89926445..89929154-chr5:89932545..89937014,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10043564	0.95[CEU][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10064606	0.80[CHB][hapmap]
rs12186867	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1316970	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1474119	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs149321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs154566	0.94[ASN][1000 genomes]
rs154569	0.82[JPT][hapmap]
rs1673381	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2366772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250366	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs250369	0.94[ASN][1000 genomes]
rs257847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs27196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs27197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28480058	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3112773	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42467	0.82[JPT][hapmap]
rs4588621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5028525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs567441	0.89[ASN][1000 genomes]
rs599432	1.00[JPT][hapmap]
rs649449	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs656679	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6891287	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6891840	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6892132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908818	0.95[CEU][hapmap];0.80[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9283789	0.92[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	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89909800-89928800	Weak transcription	Fetal Brain Female	brain
2	chr5:89910000-89928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:89914200-89928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:89918000-89950600	Weak transcription	Pancreas	Pancrea
5	chr5:89919600-89936400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:89920800-89928800	Weak transcription	Brain Anterior Caudate	brain
7	chr5:89922800-89928600	Weak transcription	Brain Germinal Matrix	brain
8	chr5:89924200-89928400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:89924400-89927800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:89925200-89936400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:89925400-89928000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:89925400-89936200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:89925400-89938600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:89925600-89928000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:89925600-89931200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:89925800-89928000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:89926200-89928400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:89926400-89929200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:89927000-89927600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:89927000-89927600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr5:89927000-89928800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:89927000-89929000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr5:89927000-89929000	Enhancers	K562	blood
24	chr5:89927000-89930400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr5:89927200-89927600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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