Variant report

Variant	rs9383914
Chromosome Location	chr6:150207234-150207235
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:150207085-150207252	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr6:150207000-150207390	MCF10A-Er-Src	breast:	n/a	chr6:150207191-150207202
3	FOS	chr6:150206927-150207411	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr6:150207022-150207308	MCF10A-Er-Src	breast:	n/a	chr6:150207191-150207202
5	FOS	chr6:150207115-150207382	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr6:150207032-150207393	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr6:150206894-150207370	MCF10A-Er-Src	breast:	n/a	chr6:150207191-150207202
8	POLR2A	chr6:150206939-150207234	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr6:150207218-150207243	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr6:150207092-150207345	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:150205939..150207450-chr6:150209753..150212132,2	K562	blood:
2	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
3	chr6:150187701..150190612-chr6:150206560..150208609,2	K562	blood:

Variant related genes	Relation type
RAET1E-AS1	TF binding region
ENSG00000268592	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000223701	Chromatin interaction
ENSG00000164520	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1334510	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2095376	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2342767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2342768	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2342769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2342770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823021	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4458704	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869764	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4870116	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6557133	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6925151	0.89[YRI][hapmap]
rs6933882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935829	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6939761	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7740145	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7742692	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7742993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744821	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7747435	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7747457	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7753544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757972	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7758033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763719	0.84[EUR][1000 genomes]
rs7763849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7764376	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7767588	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7767592	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7768626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7768665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771014	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7774787	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322225	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9322228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9371215	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9371223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9371504	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9371505	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9371533	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9371541	0.91[ASN][1000 genomes]
rs9371542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9371544	0.88[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9383577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383584	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383940	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9397058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs9397398	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9397420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs9397434	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9397438	0.85[JPT][hapmap]
rs9478192	0.81[EUR][1000 genomes]
rs9968871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986576	0.82[CEU][hapmap]

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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9383914	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9383914	RP11-350J20.9	cis	lung	GTEx
rs9383914	RP11-350J20.5	cis	Artery Tibial	GTEx
rs9383914	RP11-350J20.5	cis	Thyroid	GTEx
rs9383914	LRP11	cis	Adipose Subcutaneous	GTEx
rs9383914	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs9383914	RAET1G	cis	Thyroid	GTEx
rs9383914	RAET1G	cis	Esophagus Mucosa	GTEx
rs9383914	RP11-350J20.5	cis	lung	GTEx
rs9383914	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9383914	RAET1G	cis	Artery Tibial	GTEx
rs9383914	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9383914	RAET1E	cis	Nerve Tibial	GTEx
rs9383914	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9383914	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150202800-150208600	Weak transcription	HSMMtube	muscle
2	chr6:150205000-150210400	Enhancers	HMEC	breast
3	chr6:150205600-150207800	Weak transcription	NHDF-Ad	bronchial
4	chr6:150205600-150208200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:150205600-150208400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:150205600-150216000	Weak transcription	Right Atrium	heart
7	chr6:150205800-150208000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:150205800-150208000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:150205800-150208000	Enhancers	NHEK	skin
10	chr6:150205800-150208400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:150205800-150210200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:150205800-150216000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:150206000-150208200	Weak transcription	Esophagus	oesophagus
14	chr6:150206000-150208200	Weak transcription	NHLF	lung
15	chr6:150206000-150208800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:150206000-150216000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:150206200-150208000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:150206600-150211600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:150206800-150207400	Enhancers	A549	lung
20	chr6:150206800-150208400	Enhancers	Hela-S3	cervix

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