Variant report

Variant	rs2779556
Chromosome Location	chr9:101265290-101265291
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101262590..101265763-chr9:101267010..101270845,4	MCF-7	breast:
2	chr9:101260325..101263072-chr9:101264544..101267406,3	K562	blood:
3	chr9:101243556..101249649-chr9:101264074..101268141,6	MCF-7	breast:
4	chr9:101255431..101257396-chr9:101263161..101266108,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1184859	0.82[JPT][hapmap]
rs2095121	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2779546	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2779550	0.85[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2779557	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2779563	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2779565	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2779571	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2779575	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779577	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779579	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2779583	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779586	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779589	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779590	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2779591	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779593	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2808558	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2808565	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2808567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7024986	0.93[ASN][1000 genomes]
rs871797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831665	chr9:101170061-101367692	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv6630	chr9:101236324-101267349	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2779556	TGFBR1	cis	brain	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101258400-101266600	Weak transcription	Fetal Brain Female	brain
2	chr9:101262800-101267000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:101263800-101266200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:101263800-101267600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr9:101264000-101266600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr9:101264000-101266600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr9:101264000-101266600	Enhancers	Left Ventricle	heart
8	chr9:101264200-101265800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:101264200-101265800	Enhancers	Fetal Muscle Trunk	muscle
10	chr9:101264200-101266200	Enhancers	Placenta	Placenta
11	chr9:101264200-101266400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:101264200-101266600	Enhancers	Lung	lung
13	chr9:101264200-101266800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:101264200-101266800	Weak transcription	Brain Germinal Matrix	brain
15	chr9:101264200-101267000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr9:101264400-101265400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:101264400-101265800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr9:101264400-101265800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:101264400-101266000	Enhancers	HSMMtube	muscle
20	chr9:101264400-101266000	Enhancers	Osteobl	bone
21	chr9:101264400-101266200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:101264400-101266600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr9:101264400-101266600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:101264400-101267400	Weak transcription	K562	blood
25	chr9:101264600-101265800	Enhancers	Adipose Nuclei	Adipose
26	chr9:101264600-101265800	Enhancers	NHLF	lung
27	chr9:101264600-101266000	Enhancers	NHEK	skin
28	chr9:101264600-101266800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:101264600-101268200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr9:101264800-101265400	Enhancers	Right Ventricle	heart
31	chr9:101264800-101265400	Enhancers	HMEC	breast
32	chr9:101264800-101265800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:101264800-101265800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:101264800-101265800	Enhancers	HSMM	muscle
35	chr9:101264800-101265800	Enhancers	NH-A	brain
36	chr9:101264800-101266000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:101264800-101266000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr9:101264800-101266000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr9:101264800-101266200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:101265000-101265400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:101265000-101265600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:101265000-101265800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:101265000-101266000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:101265000-101266200	Enhancers	NHDF-Ad	bronchial
45	chr9:101265000-101266400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr9:101265000-101266600	Weak transcription	Brain Angular Gyrus	brain
47	chr9:101265000-101267800	Enhancers	H9 Cell Line	embryonic stem cell
48	chr9:101265200-101265600	Enhancers	Brain Cingulate Gyrus	brain
49	chr9:101265200-101265800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr9:101265200-101265800	Enhancers	Skeletal Muscle Male	skeletal muscle

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