Variant report

Variant	rs3088294
Chromosome Location	chr9:98734670-98734671
allele	A/G
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	JUN	chr9:98734642-98734880	HepG2	liver:	n/a	chr9:98734731-98734744
2	JUND	chr9:98734623-98734876	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ERCC6L2	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11794391	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12684118	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12684321	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1359916	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16910257	0.88[GIH][hapmap]
rs3824492	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742791	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60399336	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62562984	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs963150	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3088294	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs3088294	NCBP1	cis	cerebellum	SCAN
rs3088294	C9orf102	cis	cerebellum	SCAN
rs3088294	C9orf102	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
2	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:98695800-98742400	Weak transcription	NHLF	lung
4	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
5	chr9:98710000-98735000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:98710400-98741400	Weak transcription	Brain Anterior Caudate	brain
7	chr9:98711000-98743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
9	chr9:98719000-98738600	Weak transcription	Aorta	Aorta
10	chr9:98719000-98743800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr9:98719000-98751400	Weak transcription	Stomach Mucosa	stomach
12	chr9:98719200-98734800	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:98719200-98744000	Weak transcription	Brain Substantia Nigra	brain
14	chr9:98719200-98744400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:98719200-98749600	Weak transcription	Fetal Intestine Small	intestine
16	chr9:98719200-98749800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:98719200-98752800	Weak transcription	Pancreas	Pancrea
18	chr9:98719200-98764200	Weak transcription	Spleen	Spleen
19	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:98719400-98734800	Weak transcription	Fetal Kidney	kidney
21	chr9:98719400-98742800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:98719400-98744000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:98719400-98744000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:98719400-98767200	Weak transcription	Right Ventricle	heart
25	chr9:98719400-98771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:98719600-98743800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:98719600-98766800	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:98720000-98735600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:98722400-98747800	Weak transcription	Fetal Heart	heart
30	chr9:98723000-98734800	Weak transcription	Fetal Brain Male	brain
31	chr9:98723800-98749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:98725400-98743600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:98726400-98767800	Weak transcription	Gastric	stomach
34	chr9:98728600-98736400	Strong transcription	Dnd41	blood
35	chr9:98730000-98744400	Weak transcription	Fetal Stomach	stomach
36	chr9:98730600-98751200	Weak transcription	Small Intestine	intestine
37	chr9:98731600-98736200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:98731600-98736400	Strong transcription	Primary hematopoietic stem cells	blood
39	chr9:98731800-98735400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr9:98731800-98736800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:98732000-98735400	Strong transcription	NH-A	brain
42	chr9:98732000-98735600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr9:98732200-98747400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:98732200-98751200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:98732600-98736600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:98732600-98737000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:98732600-98737000	Strong transcription	Fetal Lung	lung
48	chr9:98732600-98741000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:98732800-98735200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr9:98732800-98736400	Strong transcription	Primary monocytes fromperipheralblood	blood

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