Variant report

Variant	rs10987963
Chromosome Location	chr9:98666080-98666081
allele	A/C
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	POLR2A	chr9:98665955-98666155	MCF10A-Er-Src	breast:	n/a	n/a
2	NFIC	chr9:98665562-98666240	ECC-1	luminal epithelium:	n/a	chr9:98665876-98665892 chr9:98665874-98665891 chr9:98665874-98665890
3	NFIC	chr9:98665576-98666192	SK-N-SH	brain:	n/a	chr9:98665876-98665892 chr9:98665874-98665891 chr9:98665874-98665890

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98637758..98639329-chr9:98663637..98666308,2	K562	blood:
2	chr9:98665770..98668209-chr9:98683792..98686437,2	K562	blood:

Variant related genes	Relation type
RNA5SP289	TF binding region
ERCC6L2	TF binding region
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10115110	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10117340	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10125109	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10512242	0.81[AMR][1000 genomes]
rs10512245	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739622	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10739705	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760189	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10760261	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10760262	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10760269	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10760679	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818574	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10818746	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10818899	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10819650	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819663	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10819668	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10819720	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10985156	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10985499	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10985769	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10988755	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988817	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10989035	0.85[AMR][1000 genomes]
rs1195130	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11998982	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12000073	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12340954	0.86[AMR][1000 genomes]
rs12343734	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12345187	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12347675	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12348051	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349742	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1327996	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327997	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289466	0.83[EUR][1000 genomes]
rs13294931	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13298093	0.81[AMR][1000 genomes]
rs13299166	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2026031	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2296858	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2405134	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2405371	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2405372	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2943532	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs589362	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs596413	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs603947	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609296	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617187	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623438	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs624075	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625105	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62559026	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62559767	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs640297	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6478977	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs649819	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs657451	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666093	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs667705	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs671058	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682682	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684455	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs686048	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689619	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689696	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689697	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs689710	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689738	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689744	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689761	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689804	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs689860	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689911	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs689986	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs690056	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690063	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690286	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs690495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690528	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs690633	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs694230	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700962	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7847393	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7847983	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852346	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7871709	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816670	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs816672	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs816673	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs816674	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs816675	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs816678	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs816680	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816682	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs816683	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs816684	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs966217	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1801890	chr9:98660433-98701801	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10987963	C9orf102	cis	multi-tissue	Pritchard
rs10987963	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs10987963	ERCC6L2	cis	Artery Tibial	GTEx
rs10987963	ERCC6L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
2	chr9:98639400-98677800	Weak transcription	Placenta	Placenta
3	chr9:98639400-98678000	Weak transcription	Ovary	ovary
4	chr9:98639600-98678000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr9:98639800-98677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:98640000-98678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:98640000-98680600	Weak transcription	Colonic Mucosa	Colon
8	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
9	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:98640200-98678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:98640400-98677800	Weak transcription	Psoas Muscle	Psoas
12	chr9:98640600-98678000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:98642600-98678000	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:98642600-98680600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:98642800-98668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:98642800-98681800	Weak transcription	Fetal Kidney	kidney
17	chr9:98644200-98670600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:98644400-98678400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:98644400-98685600	Weak transcription	Gastric	stomach
20	chr9:98644600-98670200	Weak transcription	Left Ventricle	heart
21	chr9:98644600-98678000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:98644600-98690800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:98644800-98677400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:98645600-98684200	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:98645800-98670400	Weak transcription	Brain Germinal Matrix	brain
26	chr9:98645800-98672600	Weak transcription	HUVEC	blood vessel
27	chr9:98645800-98678400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
29	chr9:98646000-98680200	Weak transcription	K562	blood
30	chr9:98646600-98667800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:98646600-98670000	Weak transcription	Adipose Nuclei	Adipose
32	chr9:98646600-98681800	Weak transcription	HSMMtube	muscle
33	chr9:98646800-98672400	Weak transcription	NHDF-Ad	bronchial
34	chr9:98647400-98672800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:98647600-98678000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:98647800-98677400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:98648200-98666200	Weak transcription	HSMM	muscle
38	chr9:98648200-98677800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:98648200-98678600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr9:98649000-98667800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:98649200-98670000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr9:98649400-98670200	Weak transcription	Fetal Lung	lung
43	chr9:98649400-98676000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr9:98649400-98694400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
46	chr9:98649600-98670000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:98649600-98677400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr9:98649600-98679000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:98649800-98667800	Weak transcription	Primary B cells from cord blood	blood
50	chr9:98649800-98677800	Weak transcription	Osteobl	bone

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