Variant report

Variant	rs9399399
Chromosome Location	chr6:142628338-142628339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142626055..142628342-chr6:142647346..142649184,2	MCF-7	breast:
2	chr6:142628313..142630816-chr6:142633666..142637433,4	MCF-7	breast:
3	chr6:142626704..142628828-chr6:142640591..142642152,2	MCF-7	breast:
4	chr6:142622268..142624499-chr6:142626683..142629679,2	K562	blood:
5	chr6:142622999..142626449-chr6:142626683..142630758,4	K562	blood:
6	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	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376683	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376684	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385991	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389982	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399398	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399400	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403377	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403378	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142624600-142629000	Weak transcription	Stomach Mucosa	stomach
2	chr6:142624800-142634000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:142624800-142651800	Weak transcription	HSMM	muscle
4	chr6:142625200-142628400	Flanking Active TSS	HUVEC	blood vessel
5	chr6:142625200-142629400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:142625600-142635400	Weak transcription	Placenta	Placenta
7	chr6:142626000-142632200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:142626000-142634200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:142626000-142650600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:142626200-142629200	Enhancers	Fetal Lung	lung
11	chr6:142626200-142631800	Weak transcription	NHEK	skin
12	chr6:142626600-142639800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:142627000-142629200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:142627000-142634800	Enhancers	Liver	Liver
15	chr6:142627200-142629000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:142627600-142628800	Flanking Active TSS	HepG2	liver
17	chr6:142627600-142629400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr6:142628000-142629800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:142628200-142628400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:142628200-142628400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr6:142628200-142628600	Active TSS	A549	lung
22	chr6:142628200-142628600	Flanking Active TSS	NHLF	lung
23	chr6:142628200-142628800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:142628200-142629000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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