Variant report

Variant	rs17189604
Chromosome Location	chr9:104364889-104364890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104364128..104365110-chr9:107444509..107445032,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10512283	0.83[EUR][1000 genomes]
rs10512284	0.83[EUR][1000 genomes]
rs10512286	0.81[EUR][1000 genomes]
rs10819954	0.83[EUR][1000 genomes]
rs10819955	0.83[EUR][1000 genomes]
rs10819956	0.83[EUR][1000 genomes]
rs10819958	0.83[EUR][1000 genomes]
rs10819959	0.83[EUR][1000 genomes]
rs10819961	0.83[EUR][1000 genomes]
rs10989572	0.83[EUR][1000 genomes]
rs10989592	0.82[EUR][1000 genomes]
rs1113384	0.86[MKK][hapmap]
rs12683273	0.93[MKK][hapmap]
rs12708308	0.81[EUR][1000 genomes]
rs1323427	0.83[EUR][1000 genomes]
rs13289501	0.83[EUR][1000 genomes]
rs1407873	0.83[EUR][1000 genomes]
rs1407874	0.83[EUR][1000 genomes]
rs1415643	1.00[CHB][hapmap]
rs16920447	0.86[MKK][hapmap]
rs17189275	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17189562	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17189821	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17197124	0.83[EUR][1000 genomes]
rs17774987	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1853447	0.83[EUR][1000 genomes]
rs34888126	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35227408	0.83[EUR][1000 genomes]
rs35569161	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4266702	0.83[EUR][1000 genomes]
rs4442195	0.83[EUR][1000 genomes]
rs4743471	0.85[MKK][hapmap];0.88[TSI][hapmap]
rs55731515	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55749212	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55838720	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56052939	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56073506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56246731	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58830774	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6479060	0.82[EUR][1000 genomes]
rs72745350	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72745355	0.88[AMR][1000 genomes];0.95[EUR][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	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	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831672	chr9:104300755-104480849	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17189604	RNF20	cis	lymphoblastoid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104362000-104387400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:104364400-104365000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr9:104364400-104365000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr9:104364400-104365200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:104364400-104365200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:104364600-104365000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr9:104364600-104365000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr9:104364600-104365000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr9:104364600-104365000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:104364600-104365000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr9:104364600-104365000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr9:104364600-104365000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr9:104364600-104365000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:104364600-104365000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:104364600-104365000	Flanking Active TSS	Brain Angular Gyrus	brain
16	chr9:104364600-104365000	Active TSS	Brain Anterior Caudate	brain
17	chr9:104364600-104365000	Active TSS	Brain Cingulate Gyrus	brain
18	chr9:104364600-104365000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:104364600-104365000	Active TSS	Brain Substantia Nigra	brain
20	chr9:104364600-104365000	Enhancers	Fetal Kidney	kidney
21	chr9:104364600-104365200	Enhancers	Liver	Liver
22	chr9:104364600-104365200	Active TSS	Brain Hippocampus Middle	brain
23	chr9:104364800-104365000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr9:104364800-104365000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr9:104364800-104365000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:104364800-104365000	Enhancers	Fetal Intestine Small	intestine
27	chr9:104364800-104365200	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr9:104364800-104368200	Weak transcription	Colonic Mucosa	Colon

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