Variant report

Variant	rs9399400
Chromosome Location	chr6:142629002-142629003
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142628313..142630816-chr6:142633666..142637433,4	MCF-7	breast:
2	chr6:142622268..142624499-chr6:142626683..142629679,2	K562	blood:
3	chr6:142622999..142626449-chr6:142626683..142630758,4	K562	blood:
4	chr6:142628297..142630973-chr6:142676608..142679458,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs9321863	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376683	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385991	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385992	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389982	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399398	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399399	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403377	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403378	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1029666	chr6:142594099-142643084	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142624800-142634000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:142624800-142651800	Weak transcription	HSMM	muscle
3	chr6:142625200-142629400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:142625600-142635400	Weak transcription	Placenta	Placenta
5	chr6:142626000-142632200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:142626000-142634200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:142626000-142650600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:142626200-142629200	Enhancers	Fetal Lung	lung
9	chr6:142626200-142631800	Weak transcription	NHEK	skin
10	chr6:142626600-142639800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:142627000-142629200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:142627000-142634800	Enhancers	Liver	Liver
13	chr6:142627600-142629400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr6:142628000-142629800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr6:142628400-142629200	Genic enhancers	HUVEC	blood vessel
16	chr6:142628600-142629200	Active TSS	NHLF	lung
17	chr6:142628800-142629400	Enhancers	HepG2	liver
18	chr6:142628800-142634600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:142629000-142629400	Enhancers	Stomach Mucosa	stomach
20	chr6:142629000-142629600	Flanking Active TSS	A549	lung
21	chr6:142629000-142631200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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