Variant report

Variant	rs546577
Chromosome Location	chr9:104172936-104172937
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:104165233..104170505-chr9:104171045..104175682,8	MCF-7	breast:
2	chr9:104171442..104174138-chr9:104174646..104177184,3	MCF-7	breast:
3	chr9:104171015..104173390-chr9:104201738..104204667,2	K562	blood:
4	chr9:104171470..104172972-chr9:104174502..104177439,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1233983	0.99[ASN][1000 genomes]
rs2777342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2777345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2777347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2777349	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4535787	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4577	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs475348	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs476046	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs480792	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs491979	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs504023	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506571	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs525998	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs535453	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554157	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs571617	0.82[JPT][hapmap]
rs577823	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs578597	0.82[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[MKK][hapmap];0.99[ASN][1000 genomes]
rs578770	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs681	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7852444	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs546577	ZNF189	trans	multi-tissue	Pritchard
rs546577	ZNF189	cis	multi-tissue	Pritchard
rs546577	ZNF189	cis	Liver	GTEx
rs546577	XPA	cis	cerebellum	SCAN
rs546577	ANKS6	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104162800-104173800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:104163000-104173000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr9:104163200-104174000	ZNF genes & repeats	Fetal Lung	lung
4	chr9:104163400-104174000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:104163600-104173600	ZNF genes & repeats	Ovary	ovary
6	chr9:104164000-104173600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:104164400-104173400	ZNF genes & repeats	Colon Smooth Muscle	Colon
8	chr9:104164600-104173600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:104164600-104173800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:104164800-104173400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr9:104164800-104174200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:104164800-104174200	ZNF genes & repeats	Brain Hippocampus Middle	brain
13	chr9:104164800-104175400	ZNF genes & repeats	Fetal Muscle Leg	muscle
14	chr9:104165000-104173800	ZNF genes & repeats	Liver	Liver
15	chr9:104165400-104173200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr9:104165400-104173600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
17	chr9:104165400-104173600	ZNF genes & repeats	HSMM	muscle
18	chr9:104165400-104176200	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr9:104165600-104178200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr9:104166200-104173000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
21	chr9:104166400-104173000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:104167000-104173200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
23	chr9:104167000-104174000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
24	chr9:104167200-104173200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:104167400-104173000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr9:104167400-104173200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
27	chr9:104167400-104173400	ZNF genes & repeats	Psoas Muscle	Psoas
28	chr9:104167400-104173600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
29	chr9:104167600-104173600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:104169000-104173600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
31	chr9:104169000-104173600	ZNF genes & repeats	Brain Germinal Matrix	brain
32	chr9:104169800-104173600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
33	chr9:104172000-104173600	Enhancers	HepG2	liver
34	chr9:104172000-104176000	Weak transcription	Aorta	Aorta
35	chr9:104172000-104177800	Weak transcription	Lung	lung
36	chr9:104172000-104179200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr9:104172000-104179400	Weak transcription	Pancreas	Pancrea
38	chr9:104172000-104180800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:104172800-104173200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr9:104172800-104175000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:104172800-104175200	Weak transcription	Fetal Brain Male	brain
42	chr9:104172800-104180800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:104172800-104181200	Weak transcription	Fetal Heart	heart
44	chr9:104172800-104187000	Weak transcription	Left Ventricle	heart

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