Variant report

Variant	rs4551980
Chromosome Location	chr15:50122868-50122869
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	chr15:49911930..49914720-chr15:50121059..50122891,3	MCF-7	breast:
2	chr15:49906396..49908796-chr15:50121690..50125085,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166262	Chromatin interaction
ENSG00000104047	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11070724	0.98[ASN][1000 genomes]
rs11070727	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070728	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070729	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070731	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634432	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634466	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634538	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11635995	0.97[ASN][1000 genomes]
rs11855340	0.97[ASN][1000 genomes]
rs11858914	0.90[ASN][1000 genomes]
rs12438404	0.94[ASN][1000 genomes]
rs12440711	0.96[ASN][1000 genomes]
rs12441351	0.93[JPT][hapmap]
rs12442186	0.96[ASN][1000 genomes]
rs12442880	0.96[ASN][1000 genomes]
rs12904515	0.95[ASN][1000 genomes]
rs12909601	0.96[ASN][1000 genomes]
rs12911756	0.98[ASN][1000 genomes]
rs12912869	0.98[ASN][1000 genomes]
rs1395882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1395883	0.95[ASN][1000 genomes]
rs1395885	0.95[ASN][1000 genomes]
rs1395886	0.94[ASN][1000 genomes]
rs1507584	0.95[ASN][1000 genomes]
rs1507585	0.95[ASN][1000 genomes]
rs1507586	0.95[ASN][1000 genomes]
rs1588122	0.95[ASN][1000 genomes]
rs1828041	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1828042	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1848282	0.95[ASN][1000 genomes]
rs1848283	0.95[ASN][1000 genomes]
rs1848284	0.95[ASN][1000 genomes]
rs2102383	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2413967	0.95[ASN][1000 genomes]
rs2413968	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2413969	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2413970	0.95[ASN][1000 genomes]
rs2413971	0.91[ASN][1000 genomes]
rs2452535	0.95[ASN][1000 genomes]
rs2452537	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452538	0.95[ASN][1000 genomes]
rs2456840	0.95[ASN][1000 genomes]
rs2456841	0.95[ASN][1000 genomes]
rs2456842	0.93[ASN][1000 genomes]
rs2660966	0.95[ASN][1000 genomes]
rs2899438	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34614239	0.95[ASN][1000 genomes]
rs34696884	0.86[ASN][1000 genomes]
rs35816674	0.96[ASN][1000 genomes]
rs35861473	0.96[ASN][1000 genomes]
rs4404008	0.97[ASN][1000 genomes]
rs4526969	0.96[ASN][1000 genomes]
rs4774546	0.95[ASN][1000 genomes]
rs4774547	0.88[ASN][1000 genomes]
rs4774548	0.85[ASN][1000 genomes]
rs71124308	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7164001	0.80[AMR][1000 genomes]
rs7182178	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182911	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8024792	0.84[EUR][1000 genomes]
rs8039234	0.97[ASN][1000 genomes]
rs873107	0.95[ASN][1000 genomes]
rs937169	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1047047	chr15:50070224-50125096	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1042311	chr15:50083175-50125096	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2761888	chr15:50083187-50125108	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4551980	CEP152	cis	cerebellum	SCAN
rs4551980	SPG11	cis	parietal	SCAN
rs4551980	PATL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50116600-50124000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:50120200-50126000	Weak transcription	Psoas Muscle	Psoas
3	chr15:50122000-50123600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50122200-50124200	Enhancers	Primary hematopoietic stem cells	blood
5	chr15:50122400-50123000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr15:50122400-50124400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:50122400-50124800	Enhancers	Adipose Nuclei	Adipose
8	chr15:50122400-50125000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:50122400-50125200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:50122600-50123000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:50122600-50123000	Enhancers	Fetal Kidney	kidney
12	chr15:50122600-50123000	Enhancers	Placenta	Placenta
13	chr15:50122600-50123200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr15:50122600-50124200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:50122600-50125200	Enhancers	NHDF-Ad	bronchial
16	chr15:50122600-50125200	Enhancers	Osteobl	bone
17	chr15:50122800-50123000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:50122800-50123400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:50122800-50123400	Weak transcription	Fetal Stomach	stomach
20	chr15:50122800-50123400	Weak transcription	NH-A	brain
21	chr15:50122800-50123600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:50122800-50124200	Enhancers	HUVEC	blood vessel
23	chr15:50122800-50124600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:50122800-50125200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:50122800-50125200	Enhancers	NHLF	lung

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