Variant report

Variant	rs9470887
Chromosome Location	chr6:38450432-38450433
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	chr6:38449509..38451131-chr6:38453879..38455476,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12200371	1.00[CEU][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs12662621	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs13194990	0.82[GIH][hapmap];0.84[TSI][hapmap]
rs13199426	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13200372	0.82[GIH][hapmap]
rs13206272	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13215683	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13218556	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13220921	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6900510	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71544422	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9462434	0.82[EUR][1000 genomes]
rs9462435	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9470876	0.82[GIH][hapmap];0.84[TSI][hapmap]
rs9470878	0.91[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs9470879	0.91[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9470884	0.91[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38437000-38455400	Weak transcription	Gastric	stomach
2	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:38445400-38452600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:38446200-38453400	Weak transcription	Primary T cells from cord blood	blood
5	chr6:38446600-38455400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:38448600-38450800	Enhancers	Fetal Brain Female	brain
7	chr6:38449000-38451000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr6:38449000-38451400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr6:38449200-38450800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:38449200-38451600	Enhancers	Psoas Muscle	Psoas
11	chr6:38449400-38451000	Enhancers	Fetal Muscle Leg	muscle
12	chr6:38449600-38450600	Enhancers	HSMMtube	muscle
13	chr6:38449600-38450800	Enhancers	Fetal Lung	lung
14	chr6:38449600-38451200	Enhancers	Fetal Stomach	stomach
15	chr6:38449800-38450600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:38449800-38451200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr6:38449800-38451600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:38449800-38452400	Enhancers	Primary B cells from cord blood	blood
19	chr6:38449800-38452400	Enhancers	Primary B cells from peripheral blood	blood
20	chr6:38449800-38461600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:38450000-38451000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:38450000-38451000	Enhancers	Fetal Brain Male	brain
23	chr6:38450000-38453200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:38450000-38461000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:38450200-38451000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr6:38450200-38452000	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:38450400-38451000	Enhancers	GM12878-XiMat	blood

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