Variant report

Variant	rs12898341
Chromosome Location	chr15:51456385-51456386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51450194..51453157-chr15:51454240..51457739,4	MCF-7	breast:
2	chr15:51453050..51456632-chr15:51484073..51486143,44	MCF-7	breast:
3	chr15:51449043..51450936-chr15:51456293..51458915,2	MCF-7	breast:
4	chr15:51451516..51454469-chr15:51455388..51457831,2	MCF-7	breast:
5	chr15:51453641..51456557-chr15:51478131..51480055,2	MCF-7	breast:
6	chr15:51455156..51457220-chr15:51483555..51485672,2	MCF-7	breast:
7	chr15:51453550..51456646-chr15:51483594..51486501,4	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1025738	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025739	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519293	0.89[ASN][1000 genomes]
rs1075680	0.82[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs11070838	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122044	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12323970	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12324478	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12324672	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442450	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904155	0.82[JPT][hapmap]
rs12904416	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915091	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438926	0.82[JPT][hapmap]
rs16964048	0.89[JPT][hapmap]
rs2278559	0.88[JPT][hapmap]
rs35665801	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4775922	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56140513	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7170009	0.82[JPT][hapmap]
rs7176579	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178516	0.81[ASN][1000 genomes]
rs7179084	0.81[ASN][1000 genomes]
rs745258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028561	0.81[ASN][1000 genomes]
rs8040954	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51453800-51462000	Weak transcription	Aorta	Aorta
2	chr15:51455000-51456400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:51455000-51456800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr15:51455000-51456800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr15:51455200-51456600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr15:51455400-51456400	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:51455400-51456600	Enhancers	Primary B cells from cord blood	blood
8	chr15:51455600-51456400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:51455600-51456400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr15:51455600-51456400	Enhancers	Right Ventricle	heart
11	chr15:51455600-51456600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:51455600-51456600	Enhancers	Placenta	Placenta
13	chr15:51455800-51456400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:51455800-51456600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr15:51455800-51456600	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr15:51455800-51456600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr15:51456000-51456400	Enhancers	Brain Hippocampus Middle	brain
18	chr15:51456000-51456400	Enhancers	Psoas Muscle	Psoas
19	chr15:51456000-51456400	Enhancers	Osteobl	bone
20	chr15:51456000-51456600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:51456000-51456600	Enhancers	HSMM	muscle
22	chr15:51456000-51461000	Weak transcription	NHDF-Ad	bronchial
23	chr15:51456200-51456400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:51456200-51456400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:51456200-51456400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr15:51456200-51456600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr15:51456200-51456600	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr15:51456200-51456600	Enhancers	HSMMtube	muscle
29	chr15:51456200-51460600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:51456200-51462200	Weak transcription	Fetal Heart	heart

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