Variant report

Variant	rs4744191
Chromosome Location	chr9:95976263-95976264
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	chr9:95962951..95965584-chr9:95975622..95978516,3	MCF-7	breast:
2	chr9:95965438..95972862-chr9:95973191..95979158,8	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12348559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553462	0.96[ASN][1000 genomes]
rs12554962	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs17594889	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34610897	1.00[ASN][1000 genomes]
rs4743910	1.00[ASN][1000 genomes]
rs4744193	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744194	0.82[CEU][hapmap]
rs4744198	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs4744199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744216	0.98[ASN][1000 genomes]
rs60604890	0.98[ASN][1000 genomes]
rs73523697	1.00[ASN][1000 genomes]
rs73527611	1.00[ASN][1000 genomes]
rs73527643	1.00[ASN][1000 genomes]
rs73527659	0.96[ASN][1000 genomes]
rs753697	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs7864826	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4744191	C9orf102	cis	parietal	SCAN
rs4744191	NGLY1	trans	multi-tissue	Pritchard
rs4744191	ZNF484	cis	cerebellum	SCAN
rs4744191	FGD3	cis	cerebellum	SCAN
rs4744191	NGLY1	cis	Liver	GTEx

Chromatin state (count:24 , 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	chr9:95969800-95976800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:95971000-95979800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:95971000-95979800	Weak transcription	Small Intestine	intestine
5	chr9:95971000-95981400	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:95971200-95985800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:95971600-95976800	Weak transcription	Fetal Brain Female	brain
8	chr9:95971600-95979600	Weak transcription	Spleen	Spleen
9	chr9:95972800-95979600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:95973000-95979600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:95974200-95985400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:95974400-95976400	Enhancers	Fetal Heart	heart
13	chr9:95974400-95986800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr9:95975000-95979800	Weak transcription	Gastric	stomach
15	chr9:95975400-95977200	Weak transcription	Fetal Intestine Small	intestine
16	chr9:95975400-95979600	Weak transcription	HepG2	liver
17	chr9:95975400-95979800	Weak transcription	Psoas Muscle	Psoas
18	chr9:95975600-95979400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:95975600-95979600	Weak transcription	Left Ventricle	heart
20	chr9:95975600-95979600	Weak transcription	Pancreas	Pancrea
21	chr9:95975600-95979600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:95975600-95979800	Weak transcription	Right Ventricle	heart
23	chr9:95975600-95979800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:95976200-95976400	Enhancers	Rectal Mucosa Donor 31	rectum

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