Variant report

Variant	rs10819720
Chromosome Location	chr9:98783788-98783789
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98636137..98638134-chr9:98783030..98785648,2	K562	blood:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10115110	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10117340	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10512245	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10739622	0.83[EUR][1000 genomes]
rs10739705	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10760189	0.81[EUR][1000 genomes]
rs10760261	0.84[EUR][1000 genomes]
rs10760262	0.84[EUR][1000 genomes]
rs10760269	0.83[EUR][1000 genomes]
rs10760679	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10818746	0.83[EUR][1000 genomes]
rs10818899	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10819650	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10819663	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10819668	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985769	0.83[EUR][1000 genomes]
rs10987963	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10988755	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10988817	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10989035	0.82[AMR][1000 genomes]
rs1195130	0.86[AMR][1000 genomes]
rs11998982	0.82[EUR][1000 genomes]
rs12000073	0.83[EUR][1000 genomes]
rs12340954	0.81[AMR][1000 genomes]
rs12343734	0.83[EUR][1000 genomes]
rs12345187	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12347675	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12348051	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12349742	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1327996	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1327997	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13299166	0.81[EUR][1000 genomes]
rs2026031	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2296858	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2405372	0.85[EUR][1000 genomes]
rs2943532	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs589362	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs596413	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs603947	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609296	0.84[EUR][1000 genomes]
rs617187	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs623438	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs624075	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs625105	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62559026	0.81[EUR][1000 genomes]
rs62559767	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs640297	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs649819	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs657451	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs666093	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs667705	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs671058	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs682682	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs684455	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs686048	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs689619	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs689696	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs689697	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689710	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs689738	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs689744	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689761	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs689804	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689860	0.81[EUR][1000 genomes]
rs689911	0.80[EUR][1000 genomes]
rs689986	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs690056	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs690063	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs690286	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690495	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs690528	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690633	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs694230	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7847393	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7847983	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs966217	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv524266	chr9:98780606-98804274	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3359379	chr9:98782656-98785504	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10819720	C9orf102	cis	multi-tissue	Pritchard
rs10819720	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98782600-98784400	Active TSS	Ovary	ovary
2	chr9:98782600-98784600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr9:98782600-98784600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:98782600-98785200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr9:98782600-98785400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:98782600-98785400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr9:98782800-98783800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
8	chr9:98782800-98783800	Active TSS	Fetal Kidney	kidney
9	chr9:98782800-98783800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr9:98782800-98784000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr9:98782800-98784000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
12	chr9:98782800-98784000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
13	chr9:98782800-98784000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:98782800-98784000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
15	chr9:98782800-98784000	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr9:98782800-98784200	Bivalent/Poised TSS	Fetal Brain Female	brain
17	chr9:98782800-98784400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:98782800-98784400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
19	chr9:98782800-98784600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
20	chr9:98782800-98784800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:98782800-98785000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
22	chr9:98782800-98785200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
23	chr9:98782800-98785200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:98783000-98783800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
25	chr9:98783000-98783800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
26	chr9:98783000-98783800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
27	chr9:98783000-98783800	Flanking Bivalent TSS/Enh	NH-A	brain
28	chr9:98783000-98784000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr9:98783000-98784000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:98783000-98784000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:98783000-98784000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr9:98783000-98784000	Bivalent/Poised TSS	HSMM	muscle
33	chr9:98783000-98784000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
34	chr9:98783000-98784000	Bivalent/Poised TSS	NHLF	lung
35	chr9:98783000-98784200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:98783000-98784400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:98783000-98784400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:98783000-98784400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:98783000-98784400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
40	chr9:98783000-98784400	Bivalent/Poised TSS	Fetal Stomach	stomach
41	chr9:98783000-98784400	Bivalent/Poised TSS	HSMMtube	muscle
42	chr9:98783000-98784600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:98783000-98784600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:98783000-98784600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:98783000-98784600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:98783000-98784600	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr9:98783000-98784600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr9:98783000-98784800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr9:98783000-98784800	Bivalent/Poised TSS	NHEK	skin
50	chr9:98783200-98783800	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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