Variant report

Variant	rs12529701
Chromosome Location	chr6:140306148-140306149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139693546..139697103-chr6:140303814..140307360,4	MCF-7	breast:
2	chr6:139688550..139692110-chr6:140303432..140306367,3	MCF-7	breast:
3	chr6:140305809..140308488-chr6:140308726..140310793,2	K562	blood:
4	chr6:139694032..139697132-chr6:140304590..140307276,4	MCF-7	breast:
5	chr6:140299794..140302085-chr6:140302801..140306484,3	K562	blood:
6	chr6:139695253..139697134-chr6:140305426..140307946,2	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1028471	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10499216	0.84[ASN][1000 genomes]
rs10499219	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11967326	0.82[AFR][1000 genomes]
rs12523886	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12528420	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12529920	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1390500	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1572674	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17069706	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17069710	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17069727	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17069741	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17069805	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1879097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2050716	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2328026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs36026965	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60747543	0.85[EUR][1000 genomes]
rs62429482	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62429486	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62429513	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62429521	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62429525	0.82[ASN][1000 genomes]
rs62431062	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62431064	0.86[EUR][1000 genomes]
rs62431065	0.86[EUR][1000 genomes]
rs62431066	0.84[EUR][1000 genomes]
rs6915764	0.83[EUR][1000 genomes]
rs732015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs73569508	0.85[AFR][1000 genomes]
rs73571530	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7770431	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9484329	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9484331	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9484332	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 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	chr6:140298200-140306200	Enhancers	Hela-S3	cervix
2	chr6:140300600-140306600	Enhancers	Placenta	Placenta
3	chr6:140301000-140306200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:140301000-140306200	Enhancers	NHDF-Ad	bronchial
5	chr6:140302600-140306200	Enhancers	Fetal Intestine Large	intestine
6	chr6:140302800-140311000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:140304200-140310600	Weak transcription	Small Intestine	intestine
8	chr6:140304200-140311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr6:140304200-140312000	Weak transcription	Fetal Brain Male	brain
10	chr6:140304400-140306400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr6:140304800-140306200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr6:140304800-140311800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:140305000-140306200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:140305000-140311400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:140305200-140311000	Weak transcription	Fetal Kidney	kidney
16	chr6:140305200-140311000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:140305200-140311200	Weak transcription	Adipose Nuclei	Adipose
18	chr6:140305400-140310800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:140305600-140309600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:140305600-140311200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:140305600-140317200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:140305800-140311200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:140305800-140311200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:140305800-140311200	Weak transcription	Osteobl	bone
25	chr6:140305800-140311400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:140305800-140312000	Weak transcription	HSMM	muscle
27	chr6:140305800-140312200	Weak transcription	Ovary	ovary
28	chr6:140305800-140312200	Weak transcription	HSMMtube	muscle
29	chr6:140306000-140309800	Weak transcription	NHLF	lung

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