Variant report

Variant	rs7747929
Chromosome Location	chr6:100871488-100871489
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	chr6:100869406..100871718-chr6:100874108..100875813,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228082	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12662778	0.81[ASN][1000 genomes]
rs13211871	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1395119	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1472799	0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1546393	0.87[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs17060530	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876156	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1876157	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2032511	0.84[ASN][1000 genomes]
rs2202537	0.87[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs34501046	0.81[ASN][1000 genomes]
rs3734357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778037	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3778038	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap]
rs3778040	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs3798499	0.91[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798509	0.81[ASN][1000 genomes]
rs9390345	0.81[ASN][1000 genomes]
rs9403740	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv515895	chr6:100868779-100910798	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100831200-100874000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr6:100838400-100874800	Weak transcription	Psoas Muscle	Psoas
3	chr6:100839400-100874200	Weak transcription	HSMM	muscle
4	chr6:100856800-100874800	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:100862200-100890600	Weak transcription	Adipose Nuclei	Adipose
6	chr6:100863000-100894600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:100864000-100887000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:100867400-100889000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:100868800-100874200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:100869000-100874000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:100869000-100874200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:100869000-100882200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:100869200-100873800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:100869200-100874600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:100869400-100874200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:100869400-100882200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:100869600-100874000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:100869600-100874200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:100869600-100874400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:100870400-100871600	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr6:100871400-100871800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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