Variant report

Variant	rs10818899
Chromosome Location	chr9:98622411-98622412
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10115110	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10117340	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10125109	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10512245	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10739622	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739705	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10760189	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10760261	0.94[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760262	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760269	0.94[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760679	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10818574	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10818746	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819650	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10819663	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10819668	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10819720	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10985156	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10985499	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10985769	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10987963	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10988755	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10988817	0.89[CEU][hapmap];0.87[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10989035	0.83[AMR][1000 genomes]
rs1195130	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11998982	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12000073	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340954	0.86[AMR][1000 genomes]
rs12343734	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345187	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12347675	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12348051	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12349742	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327996	0.80[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1327997	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13289466	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13294931	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13299166	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2026031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296858	0.87[AMR][1000 genomes]
rs2405134	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2405371	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2405372	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2943532	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs589362	0.89[CEU][hapmap];0.87[CHB][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs596413	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs603947	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs609296	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs617187	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs623438	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs624075	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs625105	0.89[CEU][hapmap];0.83[CHB][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62559026	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62559767	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs640297	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6478977	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs649819	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs657451	0.89[CEU][hapmap];0.82[CHB][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs666093	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs667705	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs671058	0.89[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs682682	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]
rs684455	0.89[CEU][hapmap];0.87[CHB][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs686048	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs689619	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689696	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs689697	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689710	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs689738	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689744	0.87[AMR][1000 genomes]
rs689761	0.89[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs689804	0.94[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689860	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs689911	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689986	0.94[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs690056	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690063	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690286	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs690495	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs690528	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs690633	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694230	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs700962	0.94[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7847393	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7847983	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7852346	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7871709	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs816670	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816672	0.94[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816673	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816674	0.94[CHB][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816675	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816677	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs816678	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816680	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816682	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs816683	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]
rs816684	0.94[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs966217	0.94[AMR][1000 genomes];0.93[EUR][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	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
4	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10818899	LOC375748	cis	multi-tissue	Pritchard
rs10818899	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs10818899	ERCC6L2	cis	Adipose Subcutaneous	GTEx
rs10818899	C9orf102	cis	multi-tissue	Pritchard
rs10818899	ERCC6L2	cis	Artery Tibial	GTEx
rs10818899	LOC286353	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98602000-98632800	Weak transcription	Left Ventricle	heart
2	chr9:98602000-98636000	Weak transcription	Lung	lung
3	chr9:98610200-98636200	Weak transcription	Brain Germinal Matrix	brain
4	chr9:98610200-98636800	Weak transcription	Gastric	stomach
5	chr9:98613400-98632800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:98615200-98624400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:98615400-98624000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:98617000-98634200	Weak transcription	Fetal Kidney	kidney
9	chr9:98619800-98633000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:98619800-98633800	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:98620000-98626400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:98620200-98624000	Weak transcription	NHLF	lung
13	chr9:98620400-98624400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:98620400-98636200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:98620600-98636600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:98620800-98624600	Weak transcription	Primary B cells from cord blood	blood
17	chr9:98621000-98636400	Weak transcription	Hela-S3	cervix

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