Variant report

Variant	rs7756850
Chromosome Location	chr6:150212596-150212597
allele	C/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	FOS	chr6:150212536-150212771	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr6:150212490-150212774	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr6:150212570-150212634	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr6:150212571-150212706	MCF10A-Er-Src	breast:	n/a	n/a
5	E2F4	chr6:150212524-150212724	MCF10A-Er-Src	breast:	n/a	n/a
6	FOXA2	chr6:150212432-150212900	A549	lung:	n/a	n/a
7	STAT3	chr6:150212575-150212608	MCF10A-Er-Src	breast:	n/a	n/a
8	FOSL2	chr6:150212371-150212702	A549	lung:	n/a	n/a
9	FOS	chr6:150212480-150212776	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr6:150212494-150212773	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
2	chr6:150212160..150213980-chr6:150214968..150218117,3	K562	blood:

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

Extended variants
information (count: 66 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs1334510	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2095376	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2342767	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]
rs2342768	0.87[EUR][1000 genomes]
rs2342769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2342770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823021	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458704	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs4869763	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]
rs4869764	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870116	0.91[EUR][1000 genomes]
rs6557133	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6933882	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]
rs6935829	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6939761	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740145	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742692	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744821	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7747435	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7747457	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753544	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757972	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758020	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]
rs7758033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7763719	0.83[EUR][1000 genomes]
rs7763849	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]
rs7764376	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767588	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7767592	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7768626	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]
rs7768665	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769118	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]
rs7771014	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7774787	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322225	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9322228	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]
rs9371215	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9371223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9371504	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371505	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371533	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9371541	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9371542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9371544	0.88[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9383577	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]
rs9383584	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383912	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383913	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383914	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]
rs9383921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383940	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs9397058	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]
rs9397398	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9397420	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]
rs9397434	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397438	0.85[JPT][hapmap]
rs9478192	0.80[EUR][1000 genomes]
rs9968871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9969044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9986576	0.82[CEU][hapmap]

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	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
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7756850	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs7756850	RP11-350J20.5	cis	Thyroid	GTEx
rs7756850	RAET1E	cis	Esophagus Mucosa	GTEx
rs7756850	RAET1G	cis	Heart Left Ventricle	GTEx
rs7756850	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs7756850	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs7756850	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs7756850	RAET1E	cis	Nerve Tibial	GTEx
rs7756850	LRP11	cis	Adipose Subcutaneous	GTEx
rs7756850	RAET1G	cis	Skin Sun Exposed Lower leg	GTEx
rs7756850	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs7756850	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs7756850	RAET1G	cis	Thyroid	GTEx
rs7756850	RP11-350J20.9	cis	lung	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150205600-150216000	Weak transcription	Right Atrium	heart
2	chr6:150205800-150216000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:150206000-150216000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:150208400-150212600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr6:150208400-150212600	Flanking Active TSS	Hela-S3	cervix
6	chr6:150209200-150212800	Enhancers	A549	lung
7	chr6:150209600-150215800	Weak transcription	Adipose Nuclei	Adipose
8	chr6:150209600-150216000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:150209600-150222200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:150210600-150212800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:150211200-150212600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:150211400-150212600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr6:150211400-150212600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:150211600-150212600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:150211600-150212600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:150211600-150212800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:150211600-150212800	Enhancers	NHDF-Ad	bronchial
18	chr6:150211600-150212800	Enhancers	Osteobl	bone
19	chr6:150211800-150212600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:150211800-150212600	Enhancers	Esophagus	oesophagus
21	chr6:150212000-150212800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr6:150212000-150212800	Enhancers	HSMM	muscle
23	chr6:150212000-150213200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:150212000-150216000	Weak transcription	Placenta	Placenta
25	chr6:150212000-150216000	Weak transcription	Lung	lung
26	chr6:150212000-150216000	Weak transcription	Ovary	ovary
27	chr6:150212000-150216000	Weak transcription	Psoas Muscle	Psoas
28	chr6:150212000-150216200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:150212200-150212800	Enhancers	NHEK	skin
30	chr6:150212200-150213200	Enhancers	HMEC	breast
31	chr6:150212200-150215800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:150212200-150215800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:150212400-150212600	Enhancers	HSMMtube	muscle
34	chr6:150212400-150212800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:150212400-150216200	Weak transcription	Fetal Muscle Leg	muscle

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