Variant report

Variant	rs9696691
Chromosome Location	chr9:95984754-95984755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95895227..95897412-chr9:95984058..95986307,4	MCF-7	breast:
2	chr9:95969627..95972419-chr9:95984512..95987236,2	MCF-7	breast:
3	chr9:95984475..95986803-chr9:96213565..96215408,2	MCF-7	breast:
4	chr9:95961414..95965641-chr9:95984083..95987391,7	MCF-7	breast:
5	chr9:95984275..95988045-chr9:96050195..96053603,3	MCF-7	breast:
6	chr9:95980802..95983532-chr9:95984355..95985930,2	MCF-7	breast:
7	chr9:95969895..95975601-chr9:95984404..95988658,5	MCF-7	breast:
8	chr9:95984628..95986573-chr9:95997782..95999959,2	MCF-7	breast:
9	chr9:95984750..95986357-chr9:96003461..96005146,2	MCF-7	breast:
10	chr9:95946365..95948119-chr9:95984241..95985758,2	MCF-7	breast:
11	chr9:95984333..95987281-chr9:96026818..96031361,4	MCF-7	breast:
12	chr9:95983716..95985400-chr9:96057478..96060069,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000165238	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10739945	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs10761210	0.92[TSI][hapmap]
rs10992685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992701	0.80[JPT][hapmap];0.96[TSI][hapmap]
rs11788911	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11790111	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12683147	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34795796	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4617217	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs56154239	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7029773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7031132	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[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7032194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7041398	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7048527	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[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7865467	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9696691	GADD45G	cis	cerebellum	SCAN
rs9696691	PTCH1	cis	cerebellum	SCAN
rs9696691	C9orf89	cis	cerebellum	SCAN

Chromatin state (count:37 , 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	chr9:95971200-95985800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:95974200-95985400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:95974400-95986800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:95978800-95985400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:95979600-95986400	Enhancers	Fetal Heart	heart
7	chr9:95979600-95992200	Enhancers	Left Ventricle	heart
8	chr9:95979800-95984800	Enhancers	Right Ventricle	heart
9	chr9:95980000-95985400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:95980000-95985600	Weak transcription	HepG2	liver
11	chr9:95980200-95985400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:95980200-95985600	Weak transcription	Small Intestine	intestine
13	chr9:95980600-95985400	Weak transcription	Fetal Intestine Large	intestine
14	chr9:95980600-95985400	Strong transcription	Fetal Intestine Small	intestine
15	chr9:95980600-95985400	Weak transcription	Right Atrium	heart
16	chr9:95981400-95985400	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:95981600-95989200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr9:95981800-95985600	Weak transcription	Brain Anterior Caudate	brain
19	chr9:95982400-95985400	Weak transcription	Gastric	stomach
20	chr9:95982400-95985400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:95982600-95985600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:95982600-95986800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:95982800-95985200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:95982800-95985200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:95982800-95985400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:95982800-95985400	Weak transcription	Colonic Mucosa	Colon
27	chr9:95983000-95985200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:95983000-95985600	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:95983200-95987200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr9:95983600-95985400	Weak transcription	Psoas Muscle	Psoas
31	chr9:95983600-95985800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:95983800-95984800	Weak transcription	Pancreas	Pancrea
33	chr9:95983800-95985600	Weak transcription	Spleen	Spleen
34	chr9:95984200-95985400	Weak transcription	Fetal Brain Male	brain
35	chr9:95984400-95985400	Weak transcription	Fetal Muscle Leg	muscle
36	chr9:95984400-95985400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr9:95984600-95985400	Enhancers	Hela-S3	cervix

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