Variant report

Variant	rs7865385
Chromosome Location	chr9:103247581-103247582
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103187531..103190394-chr9:103247265..103248958,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10819788	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs10989120	0.82[TSI][hapmap]
rs10989127	0.86[MEX][hapmap]
rs12003523	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12004257	0.86[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs12236970	0.82[TSI][hapmap]
rs1332598	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs17740576	0.95[GIH][hapmap]
rs17741842	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17741914	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17741974	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17742650	0.80[AMR][1000 genomes]
rs17813663	0.95[GIH][hapmap];0.93[MEX][hapmap]
rs17813801	0.95[GIH][hapmap];0.93[MEX][hapmap]
rs17814243	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17814768	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17814828	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17815616	0.80[AMR][1000 genomes]
rs1930238	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1970632	0.80[AMR][1000 genomes]
rs2026998	0.95[GIH][hapmap];0.93[MEX][hapmap]
rs2274882	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs2417179	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34400489	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3983768	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4395949	0.95[GIH][hapmap]
rs58407864	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61001412	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7033848	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7033969	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041892	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042792	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7046659	0.81[MEX][hapmap]
rs73655579	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655582	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73655584	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73655586	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73655588	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73655590	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73657324	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7861317	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7862727	1.00[CEU][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7866623	0.89[AMR][1000 genomes];1.00[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	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7865385	C9orf30	Cis_1M	lymphoblastoid	RTeQTL
rs7865385	C9orf30	cis	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103237000-103251600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:103238000-103248600	Weak transcription	Brain Hippocampus Middle	brain
3	chr9:103238200-103249000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr9:103238200-103251600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:103238200-103252000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:103238200-103264200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:103238200-103274600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:103238400-103251400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:103238400-103251400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:103238400-103251800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:103238600-103251800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:103245200-103251600	Weak transcription	Brain Substantia Nigra	brain
13	chr9:103245400-103251400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:103247000-103248000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:103247400-103247800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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