Variant report

Variant	rs1378893
Chromosome Location	chr15:51964788-51964789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51964695..51967594-chr15:51978181..51980955,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1017679	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10851501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11070861	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11857716	0.82[AMR][1000 genomes]
rs12324531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12441057	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12708427	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12901452	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12904173	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12904583	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1378892	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378894	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1378895	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1456295	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1456297	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471072	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1531157	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551657	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17524750	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17524906	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1840707	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1902595	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1902596	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2061425	0.83[AMR][1000 genomes]
rs2252220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2414112	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606137	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2606138	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606139	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606141	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2606143	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2606145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2606146	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2607110	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2607112	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2607116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607117	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2622768	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2622769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622770	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs28408214	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34448759	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34532503	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34662965	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34929849	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35011964	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4465557	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4774594	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4775954	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55725532	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60694229	0.81[AMR][1000 genomes]
rs6493507	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493511	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493512	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs716986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7180329	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7181921	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8025974	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8027162	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8029731	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs897581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956171	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9672605	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9944266	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][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	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
2	nsv904219	chr15:51851999-51977159	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
3	nsv457139	chr15:51854718-51977159	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
4	nsv569407	chr15:51854718-51977159	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
5	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51963400-51965000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:51963400-51965200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr15:51963800-51965400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:51964000-51965000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr15:51964200-51964800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:51964200-51964800	Flanking Active TSS	K562	blood
7	chr15:51964200-51965000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr15:51964200-51965000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr15:51964200-51965000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr15:51964200-51965000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr15:51964200-51965400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:51964200-51965600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:51964400-51964800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:51964400-51965400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:51964600-51964800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr15:51964600-51964800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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