Variant report

Variant	rs682682
Chromosome Location	chr9:98702262-98702263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98637509..98639412-chr9:98700188..98702295,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10115110	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10117340	0.80[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10125109	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10512242	0.81[AMR][1000 genomes]
rs10512245	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739622	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10739705	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760189	0.82[CEU][hapmap];0.87[CHB][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10760261	0.82[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10760262	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10760269	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10760679	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818574	0.82[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10818746	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10818899	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10819650	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819663	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10819668	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10819720	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10985156	0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10985499	0.81[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10985769	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10987963	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988755	0.86[CEU][hapmap];0.95[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]
rs10988817	0.86[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10989035	0.85[AMR][1000 genomes]
rs1195130	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11998982	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12000073	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12340954	0.86[AMR][1000 genomes]
rs12343734	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12345187	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12347675	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12348051	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349742	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1327996	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327997	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289466	0.82[EUR][1000 genomes]
rs13294931	0.81[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13298093	0.81[AMR][1000 genomes]
rs13299166	0.91[CHB][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026031	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2296858	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2405134	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2405371	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2405372	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2943532	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs589362	0.86[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs596413	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs603947	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609296	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617187	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623438	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs624075	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625105	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62559026	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62559767	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs640297	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6478977	0.82[CEU][hapmap];0.86[CHB][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs649819	0.86[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs657451	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666093	0.86[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs667705	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs671058	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684455	0.86[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs686048	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689619	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689696	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689697	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs689710	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689738	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689744	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs689761	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689804	0.84[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689860	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689911	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs689986	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690056	0.86[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690063	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690286	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690495	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690528	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs690633	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs694230	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700962	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7847393	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7847983	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852346	0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7871709	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816670	0.82[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816672	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816673	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816674	0.84[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816675	0.82[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816678	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816680	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs816682	0.85[AMR][1000 genomes]
rs816683	0.82[CEU][hapmap];0.87[CHB][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816684	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs966217	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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
3	nsv1035723	chr9:98701628-98734356	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs682682	LOC286353	cis	multi-tissue	Pritchard
rs682682	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs682682	C9orf102	cis	multi-tissue	Pritchard
rs682682	ERCC6L2	cis	Adipose Subcutaneous	GTEx
rs682682	ERCC6L2	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
3	chr9:98660000-98706000	Weak transcription	Fetal Heart	heart
4	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
5	chr9:98677600-98709000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:98678600-98705600	Weak transcription	Psoas Muscle	Psoas
7	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:98680800-98706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
10	chr9:98683400-98702600	Strong transcription	HSMM	muscle
11	chr9:98686400-98709000	Weak transcription	Right Ventricle	heart
12	chr9:98686400-98711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr9:98687800-98703400	Weak transcription	Hela-S3	cervix
15	chr9:98687800-98709000	Weak transcription	Lung	lung
16	chr9:98687800-98718400	Weak transcription	Stomach Mucosa	stomach
17	chr9:98687800-98726000	Weak transcription	Gastric	stomach
18	chr9:98688400-98702400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:98688600-98705800	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:98688800-98703600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr9:98689800-98703600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr9:98690400-98707000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:98690600-98709800	Weak transcription	HMEC	breast
24	chr9:98693600-98703400	Weak transcription	HepG2	liver
25	chr9:98694400-98702600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr9:98694400-98706800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr9:98694600-98708400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr9:98695200-98703800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:98695600-98718200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:98695800-98705600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr9:98695800-98709200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:98695800-98742400	Weak transcription	NHLF	lung
33	chr9:98696000-98704200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:98696200-98704000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:98696200-98709600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:98696400-98704000	Weak transcription	Placenta	Placenta
37	chr9:98696400-98704000	Weak transcription	HUVEC	blood vessel
38	chr9:98696400-98706600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:98697000-98702800	Weak transcription	Osteobl	bone
40	chr9:98697000-98703600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:98697200-98702400	Weak transcription	NHDF-Ad	bronchial
42	chr9:98697400-98704000	Weak transcription	NH-A	brain
43	chr9:98697400-98706000	Weak transcription	Fetal Brain Male	brain
44	chr9:98697800-98704000	Weak transcription	Brain Hippocampus Middle	brain
45	chr9:98697800-98707000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:98697800-98713200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:98698400-98703000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:98698400-98703600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:98698600-98702400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:98698600-98702600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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