Variant report

Variant	rs816683
Chromosome Location	chr9:98585101-98585102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98584403..98586297-chr9:98637755..98640000,3	MCF-7	breast:
2	chr9:98583596..98587083-chr9:98587311..98591492,4	MCF-7	breast:
3	chr9:98569719..98571881-chr9:98585000..98587559,2	MCF-7	breast:
4	chr9:98571797..98574683-chr9:98583300..98586661,3	MCF-7	breast:
5	chr9:98584113..98586604-chr9:98610986..98613982,2	MCF-7	breast:
6	chr9:98578285..98580022-chr9:98583507..98586457,2	MCF-7	breast:
7	chr9:98583856..98586047-chr9:98617880..98619976,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10115110	0.81[AMR][1000 genomes]
rs10117340	0.81[AMR][1000 genomes]
rs10125109	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10512245	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10739622	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739705	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10760189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760261	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10760262	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10760269	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10760679	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10818574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10818746	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10818899	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10819650	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10819663	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10819668	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10985156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985769	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10987963	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10988755	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10988817	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1195130	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11998982	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12000073	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12340954	0.80[AMR][1000 genomes]
rs12343734	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12345187	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12347675	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12348051	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12349742	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1327996	0.80[CEU][hapmap];0.86[CHB][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1327997	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13289466	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13294931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13299166	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026031	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296858	0.81[AMR][1000 genomes]
rs2405134	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405371	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2405372	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2943532	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs589362	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs596413	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs603947	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs617187	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs623438	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs624075	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs625105	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62559026	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62559767	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs640297	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6478977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs649819	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs657451	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs666093	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs667705	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs671058	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs682682	0.82[CEU][hapmap];0.87[CHB][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs684455	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs686048	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689619	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs689696	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs689697	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs689710	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs689738	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs689744	0.81[AMR][1000 genomes]
rs689761	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689804	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs689860	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689911	0.84[AMR][1000 genomes]
rs689986	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs690056	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs690063	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs690286	0.81[AMR][1000 genomes]
rs690495	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs690528	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs690633	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs694230	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs700962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7847393	0.80[AMR][1000 genomes]
rs7847983	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7852346	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7871709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816674	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816678	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816680	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816682	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs816684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966217	0.87[AMR][1000 genomes];0.87[EUR][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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs816683	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs816683	C9orf102	cis	multi-tissue	Pritchard
rs816683	LOC286353	cis	multi-tissue	Pritchard
rs816683	ERCC6L2	cis	Artery Tibial	GTEx
rs816683	ERCC6L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98570400-98585800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:98570400-98589200	Weak transcription	Left Ventricle	heart
3	chr9:98570400-98589200	Weak transcription	Right Ventricle	heart
4	chr9:98570400-98593200	Weak transcription	Gastric	stomach
5	chr9:98570400-98593800	Weak transcription	Right Atrium	heart
6	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:98573000-98585400	Weak transcription	Thymus	Thymus
8	chr9:98576000-98596000	Weak transcription	Aorta	Aorta
9	chr9:98577600-98585600	Weak transcription	Pancreas	Pancrea
10	chr9:98581800-98593800	Weak transcription	Fetal Intestine Small	intestine
11	chr9:98582400-98585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:98582600-98586000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:98583800-98586600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr9:98584200-98585800	Enhancers	Ovary	ovary
15	chr9:98584400-98586000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:98584400-98586000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr9:98584400-98586200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:98584400-98586200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:98584600-98585200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:98584600-98585800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:98584600-98585800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:98584600-98585800	Enhancers	A549	lung
23	chr9:98584600-98585800	Enhancers	Osteobl	bone
24	chr9:98584600-98586000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:98584600-98586000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:98584600-98586000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:98584600-98586000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:98584600-98586000	Flanking Active TSS	GM12878-XiMat	blood
29	chr9:98584600-98586000	Enhancers	NH-A	brain
30	chr9:98584800-98585200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr9:98584800-98585200	Enhancers	Spleen	Spleen
32	chr9:98584800-98585200	Flanking Active TSS	NHLF	lung
33	chr9:98584800-98585600	Enhancers	NHDF-Ad	bronchial
34	chr9:98584800-98585800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:98584800-98585800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:98584800-98585800	Enhancers	Placenta	Placenta
37	chr9:98584800-98585800	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr9:98584800-98585800	Enhancers	Stomach Smooth Muscle	stomach
39	chr9:98584800-98585800	Enhancers	HSMM	muscle
40	chr9:98584800-98585800	Enhancers	HSMMtube	muscle
41	chr9:98584800-98585800	Enhancers	NHEK	skin
42	chr9:98584800-98586000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:98584800-98586000	Flanking Active TSS	Hela-S3	cervix
44	chr9:98584800-98586200	Enhancers	HUVEC	blood vessel
45	chr9:98585000-98585400	Enhancers	Colon Smooth Muscle	Colon
46	chr9:98585000-98585600	Enhancers	HMEC	breast
47	chr9:98585000-98585800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr9:98585000-98585800	Enhancers	Duodenum Mucosa	Duodenum
49	chr9:98585000-98585800	Enhancers	Fetal Stomach	stomach
50	chr9:98585000-98585800	Enhancers	Fetal Thymus	thymus

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