Variant report

Variant	rs12135550
Chromosome Location	chr1:209547268-209547269
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	chr1:209538296..209539816-chr1:209546804..209548572,2	MCF-7	breast:
2	chr1:209545685..209547992-chr1:209599839..209602350,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1006316	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs1006317	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11811038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12125098	0.92[YRI][hapmap]
rs12140933	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12142844	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12142846	0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12144725	0.92[YRI][hapmap]
rs1354851	0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1354853	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs1507336	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs17014337	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs17014370	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs17014375	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs17014395	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs17014396	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs1857967	0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1986792	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4844815	0.90[JPT][hapmap]
rs55717527	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56265166	0.81[EUR][1000 genomes]
rs6667906	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6681466	0.93[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7516864	0.84[CHB][hapmap];0.81[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209535800-209550800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:209536800-209548600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:209537600-209548600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:209540400-209549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:209541200-209548600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:209542400-209548800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:209542600-209548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:209542600-209549200	Weak transcription	A549	lung
9	chr1:209543200-209548400	Weak transcription	NHLF	lung
10	chr1:209543200-209548600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:209543200-209548800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:209543400-209548400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:209543400-209548400	Weak transcription	Hela-S3	cervix
14	chr1:209543400-209548400	Weak transcription	Osteobl	bone
15	chr1:209543600-209548600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:209544000-209549000	Weak transcription	Fetal Lung	lung
17	chr1:209544400-209550200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:209544600-209548600	Weak transcription	Fetal Brain Female	brain
19	chr1:209545600-209548800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:209545600-209548800	Weak transcription	Fetal Brain Male	brain
21	chr1:209546400-209548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:209546600-209547400	Enhancers	HMEC	breast
23	chr1:209546600-209552800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:209546800-209547400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:209546800-209550600	Enhancers	NHEK	skin
26	chr1:209547000-209547400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:209547000-209547400	Enhancers	Esophagus	oesophagus
28	chr1:209547200-209547400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:209547200-209549400	Enhancers	H1 Cell Line	embryonic stem cell

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