Variant report

Variant	rs1539669
Chromosome Location	chr9:95971876-95971877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95969895..95975601-chr9:95984404..95988658,5	MCF-7	breast:
2	chr9:95961070..95962823-chr9:95969517..95972182,2	K562	blood:
3	chr9:95969627..95972419-chr9:95984512..95987236,2	MCF-7	breast:
4	chr9:95965438..95972862-chr9:95973191..95979158,8	MCF-7	breast:
5	chr9:95963232..95968490-chr9:95968804..95973983,9	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1105079	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743903	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60960429	0.87[AFR][1000 genomes]
rs6479464	0.80[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap]
rs7041800	1.00[CHD][hapmap]
rs7858813	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv614880	chr9:95930572-95978265	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3372585	chr9:95968731-95972929	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1539669	C9orf89	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95955800-95985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:95957000-95973400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:95958200-95972800	Enhancers	Left Ventricle	heart
4	chr9:95958200-95975600	Enhancers	Pancreas	Pancrea
5	chr9:95960600-95975800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:95962200-95973400	Enhancers	Right Ventricle	heart
7	chr9:95962800-95972600	Enhancers	Fetal Muscle Leg	muscle
8	chr9:95962800-95975600	Enhancers	Fetal Intestine Large	intestine
9	chr9:95963400-95972800	Enhancers	Psoas Muscle	Psoas
10	chr9:95963800-95972400	Enhancers	Right Atrium	heart
11	chr9:95965800-95973200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:95966200-95973000	Enhancers	Colonic Mucosa	Colon
13	chr9:95967600-95973200	Genic enhancers	Fetal Intestine Small	intestine
14	chr9:95968600-95972200	Enhancers	Fetal Muscle Trunk	muscle
15	chr9:95968800-95973600	Enhancers	Placenta	Placenta
16	chr9:95969200-95975200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:95969800-95976800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:95970200-95972000	Enhancers	Stomach Mucosa	stomach
19	chr9:95970200-95972800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr9:95970600-95972000	Flanking Active TSS	HepG2	liver
21	chr9:95971000-95972000	Weak transcription	Gastric	stomach
22	chr9:95971000-95972600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr9:95971000-95973000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr9:95971000-95973200	Enhancers	Fetal Heart	heart
25	chr9:95971000-95973200	Enhancers	Stomach Smooth Muscle	stomach
26	chr9:95971000-95979800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:95971000-95979800	Weak transcription	Small Intestine	intestine
28	chr9:95971000-95981400	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:95971200-95972800	Weak transcription	Lung	lung
30	chr9:95971200-95974000	Weak transcription	Fetal Kidney	kidney
31	chr9:95971200-95974800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:95971200-95985800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr9:95971600-95972000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr9:95971600-95972200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr9:95971600-95972400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:95971600-95972600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:95971600-95976800	Weak transcription	Fetal Brain Female	brain
38	chr9:95971600-95979600	Weak transcription	Spleen	Spleen
39	chr9:95971800-95972000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr9:95971800-95972200	Flanking Active TSS	Duodenum Mucosa	Duodenum

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