Variant report

Variant	rs12898529
Chromosome Location	chr15:74538763-74538764
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	chr15:74531319..74532959-chr15:74536975..74539724,2	MCF-7	breast:
2	chr15:74530832..74532774-chr15:74536942..74538994,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11629834	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632233	0.84[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs11633101	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11633321	0.86[ASN][1000 genomes]
rs11638601	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11639316	0.83[ASN][1000 genomes]
rs11858661	0.85[JPT][hapmap]
rs12904523	0.83[ASN][1000 genomes]
rs12905224	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12905234	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12905362	0.87[ASN][1000 genomes]
rs12913344	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12913651	0.85[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1564784	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs168432	0.91[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs189497	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351153	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351160	0.81[JPT][hapmap]
rs351174	0.84[ASN][1000 genomes]
rs351180	0.81[ASN][1000 genomes]
rs351181	0.81[ASN][1000 genomes]
rs3848162	0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs901128	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv904349	chr15:74500105-74542686	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv904350	chr15:74500105-74548773	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74532800-74543200	Weak transcription	Psoas Muscle	Psoas
2	chr15:74535400-74542200	Weak transcription	Right Atrium	heart
3	chr15:74535600-74542200	Weak transcription	HSMMtube	muscle
4	chr15:74535600-74543800	Weak transcription	Right Ventricle	heart
5	chr15:74536400-74539200	Enhancers	Fetal Brain Male	brain
6	chr15:74537400-74538800	Bivalent Enhancer	NH-A	brain
7	chr15:74537800-74538800	Bivalent Enhancer	Fetal Intestine Small	intestine
8	chr15:74538000-74539000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:74538000-74540800	Weak transcription	Lung	lung
10	chr15:74538000-74542800	Weak transcription	Pancreas	Pancrea
11	chr15:74538000-74543400	Weak transcription	Gastric	stomach
12	chr15:74538400-74538800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:74538400-74538800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:74538400-74538800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr15:74538400-74539000	Enhancers	Brain Germinal Matrix	brain
16	chr15:74538400-74539000	Enhancers	Fetal Kidney	kidney
17	chr15:74538400-74542000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:74538400-74542400	Weak transcription	Left Ventricle	heart
19	chr15:74538400-74542800	Weak transcription	Brain Anterior Caudate	brain
20	chr15:74538400-74542800	Weak transcription	Brain Substantia Nigra	brain
21	chr15:74538400-74543200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:74538400-74543200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:74538400-74543200	Weak transcription	Spleen	Spleen
24	chr15:74538400-74543400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:74538600-74539200	Enhancers	Fetal Brain Female	brain
26	chr15:74538600-74542600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:74538600-74542600	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:74538600-74542800	Weak transcription	Brain Angular Gyrus	brain
29	chr15:74538600-74542800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:74538600-74543000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:74538600-74543200	Weak transcription	Fetal Heart	heart
32	chr15:74538600-74544000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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