Variant report

Variant	rs7753544
Chromosome Location	chr6:150208264-150208265
allele	A/G
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	GATA3	chr6:150208263-150209032	A549	lung:	n/a	chr6:150208596-150208606 chr6:150208597-150208604 chr6:150208598-150208615 chr6:150208597-150208606 chr6:150208595-150208607
2	SMARCC1	chr6:150208250-150211123	Hela-S3	cervix:	n/a	chr6:150208765-150208774
3	POLR2A	chr6:150208138-150210950	Hela-S3	cervix:	n/a	n/a
4	FOS	chr6:150208176-150208268	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:150182126..150185111-chr6:150208101..150209742,2	K562	blood:
2	chr6:150201367..150203467-chr6:150207974..150210289,2	MCF-7	breast:
3	chr6:150182126..150186554-chr6:150208101..150210542,3	K562	blood:
4	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
5	chr6:150208190..150211087-chr6:150219720..150221224,2	MCF-7	breast:
6	chr6:150187701..150190612-chr6:150206560..150208609,2	K562	blood:
7	chr6:150182396..150187721-chr6:150207302..150210632,6	MCF-7	breast:
8	chr6:150200712..150203416-chr6:150207860..150210756,3	MCF-7	breast:

Variant related genes	Relation type
RAET1E-AS1	TF binding region
ENSG00000268592	Chromatin interaction
ENSG00000217733	Chromatin interaction
ENSG00000120256	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1334510	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2095376	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2342767	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	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2342770	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	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869763	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	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6933882	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	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]
rs7756850	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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758033	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763719	0.84[EUR][1000 genomes]
rs7763849	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[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	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	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	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	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9371541	0.91[ASN][1000 genomes]
rs9371542	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9371544	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9383577	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]
rs9383914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383921	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383940	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9397058	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[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]
rs9478192	0.81[EUR][1000 genomes]
rs9968871	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969044	0.93[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	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
rs7753544	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs7753544	RAET1G	cis	Thyroid	GTEx
rs7753544	RAET1G	cis	Artery Tibial	GTEx
rs7753544	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs7753544	RP11-350J20.9	cis	lung	GTEx
rs7753544	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs7753544	RP11-350J20.5	cis	lung	GTEx
rs7753544	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs7753544	RAET1E	cis	Nerve Tibial	GTEx
rs7753544	RP11-350J20.5	cis	Thyroid	GTEx
rs7753544	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs7753544	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs7753544	RP11-350J20.5	cis	Artery Tibial	GTEx
rs7753544	LRP11	cis	Adipose Subcutaneous	GTEx
rs7753544	RAET1G	cis	Esophagus Mucosa	GTEx

Chromatin state (count:27 , 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	chr6:150205600-150208400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:150205600-150216000	Weak transcription	Right Atrium	heart
5	chr6:150205800-150208400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:150205800-150210200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:150205800-150216000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:150206000-150208800	Weak transcription	Adipose Nuclei	Adipose
9	chr6:150206000-150216000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:150206600-150211600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:150206800-150208400	Enhancers	Hela-S3	cervix
12	chr6:150207800-150208800	Enhancers	A549	lung
13	chr6:150207800-150210600	Enhancers	NHDF-Ad	bronchial
14	chr6:150208000-150208800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:150208000-150209000	Flanking Active TSS	NHEK	skin
16	chr6:150208000-150210600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:150208000-150210600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:150208000-150210800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:150208000-150211800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:150208200-150208400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:150208200-150208400	Enhancers	Placenta	Placenta
22	chr6:150208200-150210200	Enhancers	Esophagus	oesophagus
23	chr6:150208200-150210400	Enhancers	Fetal Intestine Small	intestine
24	chr6:150208200-150210400	Enhancers	NHLF	lung
25	chr6:150208200-150210400	Enhancers	Osteobl	bone
26	chr6:150208200-150210600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr6:150208200-150210600	Enhancers	Fetal Intestine Large	intestine

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