Variant report

Variant	rs28394554
Chromosome Location	chr9:98228225-98228226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98214310..98216415-chr9:98227721..98230889,3	MCF-7	breast:
2	chr9:98227321..98228997-chr9:98229888..98232177,2	K562	blood:
3	chr9:98223555..98229775-chr9:98269693..98275962,10	K562	blood:
4	chr9:98222977..98229750-chr9:98267050..98274823,12	K562	blood:
5	chr9:98227014..98229023-chr9:98271434..98274318,2	MCF-7	breast:
6	chr9:98228127..98229820-chr9:98239088..98240889,2	K562	blood:

Variant related genes	Relation type
ENSG00000271155	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs17368876	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17369383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066836	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134721	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2274693	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28411363	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28412122	0.82[MEX][hapmap]
rs28442014	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28468571	0.82[EUR][1000 genomes]
rs28485705	0.83[EUR][1000 genomes]
rs28488553	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504341	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571635	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28633576	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28702657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831479	0.85[EUR][1000 genomes]
rs3758301	0.80[EUR][1000 genomes]
rs62558340	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9632897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9632898	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9632916	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1053762	chr9:98208542-98232120	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1047465	chr9:98217524-98228225	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv531634	chr9:98227972-98230831	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28394554	C9orf3	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
2	chr9:98221800-98232400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
4	chr9:98224000-98228800	Weak transcription	Liver	Liver
5	chr9:98224200-98228800	Weak transcription	Right Ventricle	heart
6	chr9:98224200-98229000	Weak transcription	Esophagus	oesophagus
7	chr9:98224400-98228800	Weak transcription	HepG2	liver
8	chr9:98224600-98228800	Weak transcription	Aorta	Aorta
9	chr9:98225000-98228800	Weak transcription	Lung	lung
10	chr9:98225200-98229000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:98225600-98229200	Weak transcription	Spleen	Spleen
12	chr9:98225600-98234000	Weak transcription	Right Atrium	heart
13	chr9:98225800-98228800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:98225800-98228800	Enhancers	Brain Germinal Matrix	brain
15	chr9:98225800-98229000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:98225800-98229000	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:98225800-98239600	Weak transcription	HMEC	breast
18	chr9:98225800-98239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:98225800-98244000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:98226000-98228400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:98226000-98229000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:98226000-98229000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:98226000-98229200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:98226000-98229400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
26	chr9:98226000-98251000	Weak transcription	Osteobl	bone
27	chr9:98226200-98228800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:98226200-98229000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:98226200-98229000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:98226200-98229000	Weak transcription	Colonic Mucosa	Colon
31	chr9:98226200-98229000	Weak transcription	Pancreas	Pancrea
32	chr9:98226200-98229000	Weak transcription	HSMMtube	muscle
33	chr9:98226200-98229200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr9:98226200-98229200	Weak transcription	Fetal Heart	heart
35	chr9:98226200-98229600	Weak transcription	Placenta	Placenta
36	chr9:98226200-98230200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:98226200-98230400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:98226200-98232400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr9:98226200-98238400	Weak transcription	NH-A	brain
40	chr9:98226200-98239000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr9:98226200-98239400	Weak transcription	NHEK	skin
42	chr9:98226200-98240800	Strong transcription	Fetal Intestine Large	intestine
43	chr9:98226200-98243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:98226400-98228600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:98226400-98228600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr9:98226400-98228600	Weak transcription	Fetal Brain Female	brain
48	chr9:98226400-98228800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr9:98226400-98228800	Weak transcription	NHLF	lung
50	chr9:98226400-98230200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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