Variant report

Variant	rs9394363
Chromosome Location	chr6:36558964-36558965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36557597..36560008-chr6:36645990..36649520,4	MCF-7	breast:
2	chr6:36409059..36411660-chr6:36558695..36561393,2	MCF-7	breast:
3	chr6:36510007..36526277-chr6:36558145..36566762,35	K562	blood:
4	chr6:36406846..36414829-chr6:36558734..36566025,43	K562	blood:
5	chr6:36511879..36517279-chr6:36558264..36566013,19	MCF-7	breast:
6	chr6:36522635..36525085-chr6:36558432..36560977,2	MCF-7	breast:
7	chr6:36537495..36539937-chr6:36557300..36560014,2	K562	blood:

Variant related genes	Relation type
ENSG00000112079	Chromatin interaction
ENSG00000112078	Chromatin interaction
ENSG00000124762	Chromatin interaction
ENSG00000179165	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10214849	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs10223366	0.80[EUR][1000 genomes]
rs1076931	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10807169	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947613	0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947614	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947615	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11756557	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11756969	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs12153820	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12202732	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208086	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12211825	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1406945	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1812018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1812019	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1812020	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001101	0.89[EUR][1000 genomes]
rs2145048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713987	0.81[EUR][1000 genomes]
rs56144242	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60627328	0.81[EUR][1000 genomes]
rs61211228	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6913530	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6937430	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs72852338	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72852340	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73410251	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7344	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7738559	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7738561	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7741888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743396	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7747264	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755461	0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7759778	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759933	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7760766	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7767296	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9296193	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9349001	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357217	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9357218	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366907	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9366908	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366909	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9366911	0.85[CEU][hapmap]
rs9368938	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368939	0.88[EUR][1000 genomes]
rs9368940	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368942	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9368943	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380577	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380578	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9380580	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380582	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394359	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394360	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394361	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394362	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394365	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9394363	MEGF9	trans	cerebellum	SCAN
rs9394363	GLO1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36551600-36559600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr6:36551600-36560000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr6:36551600-36560600	Weak transcription	Fetal Intestine Small	intestine
4	chr6:36553400-36561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:36553800-36561000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:36554600-36561200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:36556200-36560000	Weak transcription	K562	blood
8	chr6:36557400-36559400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:36558200-36561000	Weak transcription	Fetal Intestine Large	intestine
10	chr6:36558400-36560200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:36558400-36560200	Weak transcription	Hela-S3	cervix
12	chr6:36558400-36560600	Weak transcription	Placenta	Placenta
13	chr6:36558400-36561200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:36558400-36561200	Weak transcription	A549	lung
15	chr6:36558400-36561400	Weak transcription	HSMMtube	muscle
16	chr6:36558600-36559600	Weak transcription	HepG2	liver
17	chr6:36558600-36560200	Weak transcription	HMEC	breast
18	chr6:36558600-36561000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:36558600-36561000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:36558600-36561000	Weak transcription	Osteobl	bone
21	chr6:36558600-36561200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:36558600-36561200	Weak transcription	HSMM	muscle
23	chr6:36558600-36561200	Weak transcription	NH-A	brain
24	chr6:36558600-36561200	Weak transcription	NHEK	skin
25	chr6:36558600-36561200	Weak transcription	NHLF	lung
26	chr6:36558600-36561400	Weak transcription	NHDF-Ad	bronchial
27	chr6:36558800-36561000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:36558800-36561200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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