Variant report

Variant	rs7852735
Chromosome Location	chr9:97715088-97715089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr9:97714821-97715383	GM12891	blood:	n/a	chr9:97715138-97715151 chr9:97715043-97715056
2	CTCF	chr9:97714940-97715090	HUVEC	blood vessel:	n/a	n/a
3	KAP1	chr9:97714680-97715628	HEK293	kidney:	n/a	n/a
4	GATA3	chr9:97714847-97715237	T-47D	breast:	n/a	chr9:97714991-97715001
5	GATA2	chr9:97714855-97715544	HUVEC	blood vessel:	n/a	chr9:97714991-97715001

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97705028..97708373-chr9:97712874..97716107,3	MCF-7	breast:
2	chr9:97544453..97547031-chr9:97714390..97716009,2	MCF-7	breast:
3	chr9:97713398..97716308-chr9:97717778..97720167,2	MCF-7	breast:
4	chr9:97702356..97704660-chr9:97713620..97715867,3	MCF-7	breast:
5	chr9:97682502..97684429-chr9:97713888..97715446,2	MCF-7	breast:
6	chr9:97711544..97713336-chr9:97713597..97715255,2	MCF-7	breast:
7	chr9:97714988..97715787-chr9:97754061..97754824,3	MCF-7	breast:
8	chr9:97715071..97716656-chr9:97720006..97722665,2	MCF-7	breast:
9	chr9:97714361..97717558-chr9:97717587..97720925,3	K562	blood:
10	chr9:97544938..97546132-chr9:97714920..97715766,5	MCF-7	breast:

No data

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction

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

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

rs_ID	r²[population]
rs10512252	0.81[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs16905559	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]
rs16911849	1.00[AMR][1000 genomes]
rs1800367	0.94[MKK][hapmap]
rs1998924	1.00[AMR][1000 genomes]
rs2078379	0.95[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]
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
rs7852735	C9orf130	cis	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

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	chr9:97710000-97715200	Enhancers	Ovary	ovary
6	chr9:97710000-97715600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:97710600-97716000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr9:97710600-97716200	Enhancers	Left Ventricle	heart
9	chr9:97710600-97716800	Enhancers	Placenta	Placenta
10	chr9:97710800-97715600	Genic enhancers	HSMM	muscle
11	chr9:97711200-97715800	Enhancers	Brain Anterior Caudate	brain
12	chr9:97711200-97715800	Enhancers	Brain Substantia Nigra	brain
13	chr9:97711200-97716200	Enhancers	Fetal Muscle Leg	muscle
14	chr9:97711200-97719000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:97711400-97717400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:97711600-97715800	Enhancers	Brain Hippocampus Middle	brain
17	chr9:97711800-97715800	Enhancers	Brain Cingulate Gyrus	brain
18	chr9:97711800-97716800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr9:97712000-97715400	Enhancers	Right Ventricle	heart
20	chr9:97712000-97716000	Enhancers	HSMMtube	muscle
21	chr9:97712200-97715600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:97712400-97715400	Enhancers	Liver	Liver
23	chr9:97712400-97715400	Enhancers	Esophagus	oesophagus
24	chr9:97712400-97715400	Enhancers	Fetal Muscle Trunk	muscle
25	chr9:97712400-97715400	Enhancers	Pancreas	Pancrea
26	chr9:97712400-97715400	Enhancers	Right Atrium	heart
27	chr9:97712400-97715600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:97712400-97715600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:97712400-97715600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:97712400-97715800	Enhancers	NHDF-Ad	bronchial
31	chr9:97712600-97715400	Enhancers	Adipose Nuclei	Adipose
32	chr9:97712600-97715400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr9:97712600-97715600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr9:97712600-97715600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:97712600-97715600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr9:97712600-97715600	Enhancers	Psoas Muscle	Psoas
37	chr9:97712600-97715600	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr9:97712600-97716000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:97712600-97716000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr9:97712600-97716200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:97712600-97716400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:97712800-97715600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr9:97712800-97715800	Enhancers	Fetal Lung	lung
44	chr9:97713000-97715200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr9:97713000-97715200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr9:97713000-97715200	Enhancers	NHEK	skin
47	chr9:97713000-97715400	Enhancers	Colonic Mucosa	Colon
48	chr9:97713000-97715600	Enhancers	Fetal Thymus	thymus
49	chr9:97713000-97715600	Enhancers	NHLF	lung
50	chr9:97713000-97715800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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