Variant report

Variant	rs12142846
Chromosome Location	chr1:209560036-209560037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209538239..209540335-chr1:209559472..209561618,2	MCF-7	breast:
2	chr1:209555303..209558478-chr1:209558595..209562675,4	MCF-7	breast:
3	chr1:209554903..209565803-chr1:209600283..209609508,22	MCF-7	breast:
4	chr1:209556562..209561769-chr1:209603992..209608152,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1006316	0.83[MEX][hapmap]
rs11811038	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12125098	0.92[YRI][hapmap]
rs12135550	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]
rs12140933	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12142844	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12144725	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs1354851	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1354853	0.89[MEX][hapmap]
rs1857967	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1986792	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55717527	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60460414	0.81[AFR][1000 genomes]
rs6667906	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674793	0.89[AFR][1000 genomes]
rs6681466	0.86[CHB][hapmap]
rs74155478	0.83[AFR][1000 genomes]

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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209549800-209560400	Weak transcription	HSMM	muscle
2	chr1:209550200-209560600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:209553200-209568600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:209555200-209561000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:209555400-209560800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr1:209555400-209561000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:209555600-209564400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:209555800-209565200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:209556600-209560800	Weak transcription	Esophagus	oesophagus
10	chr1:209556800-209560800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:209557000-209560600	Weak transcription	Placenta	Placenta
12	chr1:209557000-209560800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:209557000-209560800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:209557200-209561600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:209557400-209560800	Weak transcription	Osteobl	bone
16	chr1:209557800-209561200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:209557800-209565200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:209558000-209562000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:209558000-209566200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:209558200-209560400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:209558200-209560600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:209558200-209564400	Enhancers	HMEC	breast
23	chr1:209558400-209560600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:209558400-209564400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:209559000-209560400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:209559000-209560800	Weak transcription	HSMMtube	muscle
27	chr1:209559200-209560600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:209559400-209561200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:209559400-209565200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:209559400-209566000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:209559600-209560600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:209559800-209560200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:209560000-209560400	Enhancers	NHEK	skin
34	chr1:209560000-209563000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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