Variant report

Variant	rs16905559
Chromosome Location	chr9:97717655-97717656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr9:97717440-97718005	ECC-1	luminal epithelium:	n/a	chr9:97717721-97717738 chr9:97717722-97717736 chr9:97717718-97717736 chr9:97717718-97717735 chr9:97717720-97717733 chr9:97717718-97717732

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97683719..97685976-chr9:97715516..97717826,3	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10512252	0.95[LWK][hapmap];1.00[MKK][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16911849	1.00[AMR][1000 genomes]
rs1800367	0.94[MKK][hapmap]
rs1998924	1.00[AMR][1000 genomes]
rs2078379	0.82[LWK][hapmap];1.00[MKK][hapmap]
rs4647503	1.00[AMR][1000 genomes]
rs4647538	1.00[AMR][1000 genomes]
rs4647542	1.00[AMR][1000 genomes]
rs56340483	1.00[AMR][1000 genomes]
rs7035812	1.00[AMR][1000 genomes]
rs7039870	1.00[AMR][1000 genomes]
rs7041865	1.00[AMR][1000 genomes]
rs73657015	1.00[AMR][1000 genomes]
rs73657016	1.00[AMR][1000 genomes]
rs7852735	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7853854	1.00[AMR][1000 genomes]
rs7868690	1.00[AMR][1000 genomes]
rs7875215	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16905559	C9orf130	cis	lymphoblastoid	seeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97700200-97718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:97708800-97720000	Weak transcription	K562	blood
4	chr9:97709200-97730400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:97711200-97719000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:97713200-97720400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:97713400-97718400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:97713400-97726200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:97713800-97718200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:97713800-97757400	Weak transcription	Fetal Brain Female	brain
11	chr9:97714200-97734200	Weak transcription	Lung	lung
12	chr9:97714200-97735800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:97714600-97717800	Weak transcription	Fetal Intestine Small	intestine
14	chr9:97715000-97717800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:97715000-97718600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:97715000-97735600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:97715000-97758200	Weak transcription	Spleen	Spleen
18	chr9:97715200-97718400	Weak transcription	GM12878-XiMat	blood
19	chr9:97715200-97732200	Weak transcription	Ovary	ovary
20	chr9:97715200-97734600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:97715200-97748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:97715400-97717800	Weak transcription	Primary B cells from cord blood	blood
23	chr9:97715400-97717800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:97715400-97717800	Weak transcription	Fetal Stomach	stomach
25	chr9:97715400-97717800	Weak transcription	Pancreas	Pancrea
26	chr9:97715400-97718600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:97715400-97718800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr9:97715400-97719000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:97715400-97719600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:97715400-97723400	Weak transcription	Esophagus	oesophagus
31	chr9:97715400-97735800	Weak transcription	Right Ventricle	heart
32	chr9:97715400-97741200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr9:97715400-97749600	Weak transcription	Thymus	Thymus
34	chr9:97715600-97717800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:97715600-97717800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:97715600-97717800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:97715600-97717800	Weak transcription	Aorta	Aorta
38	chr9:97715600-97717800	Weak transcription	Fetal Intestine Large	intestine
39	chr9:97715600-97717800	Weak transcription	Osteobl	bone
40	chr9:97715600-97718200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:97715600-97718400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr9:97715600-97718400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr9:97715600-97718600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:97715600-97719800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr9:97715600-97720000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:97715600-97721000	Strong transcription	HSMM	muscle
47	chr9:97715600-97724200	Weak transcription	NHLF	lung
48	chr9:97715600-97730000	Weak transcription	Hela-S3	cervix
49	chr9:97715600-97742000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr9:97715600-97742000	Weak transcription	Psoas Muscle	Psoas

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