Variant report

Variant	rs9409665
Chromosome Location	chr9:95078723-95078724
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	chr9:95072066..95074170-chr9:95076840..95080012,3	MCF-7	breast:
2	chr9:95060850..95063689-chr9:95077337..95079160,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198000	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10125510	0.93[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1058726	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1058751	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10733744	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10761159	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1144933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152760	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152761	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152762	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1175737	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1175923	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1175929	0.84[EUR][1000 genomes]
rs1175930	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1175931	0.87[CEU][hapmap]
rs11787696	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11789578	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11790257	0.86[ASN][1000 genomes]
rs11791931	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs11792542	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11793505	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11794966	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12555097	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2084289	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296665	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs230223	0.88[EUR][1000 genomes]
rs2398749	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2761680	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3894058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs41276829	0.81[AMR][1000 genomes]
rs41280213	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41280215	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs472163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743862	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4743864	0.86[ASN][1000 genomes]
rs4743866	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs4743867	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743868	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4743871	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744123	0.86[ASN][1000 genomes]
rs4744124	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744125	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs501814	1.00[ASW][hapmap];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[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556155	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs557066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55894730	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56110031	0.86[ASN][1000 genomes]
rs56308715	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56374228	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6479421	0.93[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7042199	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs710161	1.00[LWK][hapmap]
rs7864453	0.93[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs895639	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9409464	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9409465	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9409466	0.87[CEU][hapmap]
rs9409467	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9409469	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[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409470	0.85[ASN][1000 genomes]
rs9409659	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409660	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409661	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409662	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9409663	0.81[ASN][1000 genomes]
rs9409666	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944949	0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1045165	chr9:95057462-95138564	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9409665	ANKRD19	cis	parietal	SCAN
rs9409665	C9orf79	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95056800-95086800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:95057000-95087000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:95058000-95086200	Weak transcription	Stomach Mucosa	stomach
4	chr9:95058200-95085800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:95058400-95085600	Strong transcription	Placenta	Placenta
6	chr9:95058400-95085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:95058400-95085800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:95058400-95086200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:95058600-95085800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:95058600-95085800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:95059200-95085600	Strong transcription	Duodenum Mucosa	Duodenum
12	chr9:95059200-95085600	Strong transcription	Fetal Intestine Large	intestine
13	chr9:95059200-95085800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:95059200-95085800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:95059400-95085600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:95059400-95085600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:95059400-95085800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:95059400-95085800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:95059600-95085600	Strong transcription	Primary T cells from cord blood	blood
20	chr9:95060000-95085600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr9:95060200-95083200	Strong transcription	Fetal Muscle Leg	muscle
22	chr9:95062000-95081200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:95062200-95085800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr9:95062800-95083600	Strong transcription	Primary B cells from cord blood	blood
25	chr9:95072000-95085800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:95072600-95079200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:95073000-95078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr9:95073000-95081200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:95073200-95079200	Weak transcription	Esophagus	oesophagus
30	chr9:95073200-95086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:95073400-95078800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr9:95073400-95078800	Weak transcription	Right Ventricle	heart
33	chr9:95073400-95079200	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:95073600-95078800	Weak transcription	Colonic Mucosa	Colon
35	chr9:95073600-95079200	Weak transcription	Pancreas	Pancrea
36	chr9:95073800-95078800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:95074200-95079600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr9:95074800-95082000	Weak transcription	Psoas Muscle	Psoas
39	chr9:95075000-95078800	Weak transcription	Fetal Intestine Small	intestine
40	chr9:95075000-95079200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:95075000-95085600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr9:95075200-95085600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:95075400-95082400	Strong transcription	Fetal Lung	lung
44	chr9:95075400-95085600	Strong transcription	Adipose Nuclei	Adipose
45	chr9:95075400-95085600	Strong transcription	Brain Hippocampus Middle	brain
46	chr9:95075400-95085800	Strong transcription	Fetal Thymus	thymus
47	chr9:95075400-95086200	Strong transcription	A549	lung
48	chr9:95075600-95083000	Strong transcription	Fetal Brain Female	brain
49	chr9:95075600-95085800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr9:95075600-95085800	Strong transcription	NH-A	brain

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