Variant report

Variant	rs1550243
Chromosome Location	chr2:133811842-133811843
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	chr2:133811077..133813218-chr2:133838444..133841047,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10166379	0.86[JPT][hapmap]
rs10195506	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1370594	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1370596	0.86[JPT][hapmap]
rs1437895	0.83[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs1437907	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1437910	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1550244	1.00[JPT][hapmap]
rs1595416	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs1866189	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2217747	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs4954024	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4954025	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722091	0.85[JPT][hapmap]
rs7567201	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7588709	1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv916805	chr2:133664765-133924973	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv834381	chr2:133722671-133897994	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv834382	chr2:133728399-133891418	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999703	chr2:133734955-133817962	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535926	chr2:133734955-133817962	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv875139	chr2:133777866-133929225	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv949546	chr2:133798832-133933491	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv470487	chr2:133811842-133875512	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1550243	MCM6	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133802600-133813600	Weak transcription	Ovary	ovary
2	chr2:133807600-133812000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:133810400-133812000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:133810600-133812000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:133810800-133812000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:133810800-133812000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr2:133810800-133812000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr2:133810800-133812000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:133810800-133813000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:133811000-133812000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:133811000-133812400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:133811000-133823600	Weak transcription	Fetal Brain Male	brain
13	chr2:133811200-133812000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:133811200-133812200	Enhancers	Brain Hippocampus Middle	brain
15	chr2:133811200-133812400	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr2:133811600-133812200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:133811600-133812200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:133811600-133812200	Enhancers	Stomach Smooth Muscle	stomach
19	chr2:133811800-133812000	Enhancers	Brain Anterior Caudate	brain
20	chr2:133811800-133812000	Enhancers	Brain Substantia Nigra	brain
21	chr2:133811800-133812200	Enhancers	Rectal Smooth Muscle	rectum

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