Variant report

Variant	rs6925151
Chromosome Location	chr6:150210723-150210724
allele	C/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	chr6:150210456-150210800	MCF10A-Er-Src	breast:	n/a	n/a
2	SP1	chr6:150210443-150210924	A549	lung:	n/a	n/a
3	SP1	chr6:150210279-150210893	A549	lung:	n/a	n/a
4	FOS	chr6:150210466-150210809	MCF10A-Er-Src	breast:	n/a	n/a
5	BRCA1	chr6:150209949-150210829	Hela-S3	cervix:	n/a	n/a
6	FOS	chr6:150210504-150210808	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr6:150209881-150210907	Hela-S3	cervix:	n/a	chr6:150210177-150210191 chr6:150210207-150210214
8	TAF1	chr6:150210484-150210821	Hela-S3	cervix:	n/a	n/a
9	SMARCC1	chr6:150208250-150211123	Hela-S3	cervix:	n/a	chr6:150208765-150208774
10	STAT3	chr6:150210518-150210780	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr6:150210381-150210871	Hela-S3	cervix:	n/a	n/a
12	TCF12	chr6:150210290-150210927	A549	lung:	n/a	n/a
13	MAX	chr6:150209242-150210893	Hela-S3	cervix:	n/a	n/a
14	NFYB	chr6:150210431-150210819	Hela-S3	cervix:	n/a	n/a
15	STAT3	chr6:150209916-150210828	Hela-S3	cervix:	n/a	chr6:150210314-150210326
16	CREB1	chr6:150210538-150210756	A549	lung:	n/a	n/a
17	CEBPB	chr6:150209208-150210929	Hela-S3	cervix:	n/a	chr6:150209470-150209481
18	POLR2A	chr6:150209339-150210780	MCF10A-Er-Src	breast:	n/a	n/a
19	USF2	chr6:150209204-150210912	Hela-S3	cervix:	n/a	chr6:150209928-150209939
20	POLR2A	chr6:150210374-150210854	Hela-S3	cervix:	n/a	n/a
21	MYC	chr6:150210521-150210792	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr6:150208138-150210950	Hela-S3	cervix:	n/a	n/a
23	TFAP2C	chr6:150209215-150210815	Hela-S3	cervix:	n/a	n/a
24	STAT3	chr6:150209905-150210827	MCF10A-Er-Src	breast:	n/a	chr6:150210314-150210326
25	CEBPB	chr6:150210475-150210841	A549	lung:	n/a	n/a
26	ELK1	chr6:150210296-150210901	Hela-S3	cervix:	n/a	n/a
27	ZKSCAN1	chr6:150210050-150210871	Hela-S3	cervix:	n/a	n/a
28	STAT3	chr6:150210475-150210784	MCF10A-Er-Src	breast:	n/a	n/a
29	MAZ	chr6:150209939-150210884	Hela-S3	cervix:	n/a	n/a
30	RFX5	chr6:150209898-150210832	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr6:150208350-150212272	Hela-S3	cervix:	n/a	n/a
32	CHD2	chr6:150209928-150210882	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr6:150209922-150211116	Hela-S3	cervix:	n/a	n/a
34	RAD21	chr6:150210480-150210873	Hela-S3	cervix:	n/a	n/a
35	NFYA	chr6:150210261-150211004	Hela-S3	cervix:	n/a	n/a
36	MXI1	chr6:150209237-150211154	Hela-S3	cervix:	n/a	n/a
37	FOS	chr6:150210531-150210810	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr6:150208398-150212270	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr6:150210448-150210825	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr6:150209835-150211059	Hela-S3	cervix:	n/a	n/a
41	CREB1	chr6:150210445-150210743	A549	lung:	n/a	n/a
42	FOS	chr6:150210454-150210765	MCF10A-Er-Src	breast:	n/a	n/a
43	MAFK	chr6:150210022-150210862	Hela-S3	cervix:	n/a	n/a
44	EP300	chr6:150210297-150210897	A549	lung:	n/a	n/a
45	TCF7L2	chr6:150208360-150211113	Hela-S3	cervix:	n/a	n/a
46	FOXA2	chr6:150210469-150210980	A549	lung:	n/a	n/a
47	SMC3	chr6:150209264-150210884	Hela-S3	cervix:	n/a	n/a
48	TBP	chr6:150209194-150210904	Hela-S3	cervix:	n/a	n/a
49	GTF2F1	chr6:150209210-150210886	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
2	chr6:150208190..150211087-chr6:150219720..150221224,2	MCF-7	breast:
3	chr6:150200712..150203416-chr6:150207860..150210756,3	MCF-7	breast:

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

Extended variants
information (count: 50 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10457852	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12204653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12210822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12527391	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12528243	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1855572	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1999632	0.94[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1999633	0.88[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2342766	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2342767	0.93[YRI][hapmap]
rs3798763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922946	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3922947	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4473864	0.84[ASN][1000 genomes]
rs4869755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869763	0.93[YRI][hapmap]
rs4869767	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4869768	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4870078	1.00[CEU][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4870110	0.84[ASN][1000 genomes]
rs4870117	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4870118	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5024811	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57894361	0.86[EUR][1000 genomes]
rs6557165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6912330	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6933882	0.93[YRI][hapmap]
rs7452592	0.87[EUR][1000 genomes]
rs7757984	0.88[YRI][hapmap]
rs7758020	0.89[YRI][hapmap]
rs7763849	0.89[YRI][hapmap]
rs7764677	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7768626	0.89[YRI][hapmap]
rs915140	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9322228	0.93[YRI][hapmap]
rs9322229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9371228	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9383577	0.89[YRI][hapmap]
rs9383914	0.89[YRI][hapmap]
rs9383941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9397058	0.89[YRI][hapmap]
rs9397070	0.92[EUR][1000 genomes]
rs9397420	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv819758	chr6:150210602-150210846	Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6925151	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs6925151	SHPRH	cis	cerebellum	SCAN
rs6925151	LRP11	cis	cerebellum	SCAN
rs6925151	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs6925151	RP11-350J20.5	cis	lung	GTEx
rs6925151	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs6925151	RP11-350J20.5	cis	Thyroid	GTEx
rs6925151	RP11-350J20.5	cis	Artery Tibial	GTEx
rs6925151	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs6925151	LATS1	cis	cerebellum	SCAN
rs6925151	LRP11	cis	parietal	SCAN
rs6925151	NUP43	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 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	chr6:150206600-150211600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:150208000-150210800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:150208000-150211800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:150208400-150211400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:150208400-150211600	Weak transcription	Placenta	Placenta
9	chr6:150208400-150212600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:150208400-150212600	Flanking Active TSS	Hela-S3	cervix
11	chr6:150208600-150211400	Enhancers	HSMMtube	muscle
12	chr6:150209200-150212200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:150209200-150212800	Enhancers	A549	lung
14	chr6:150209400-150211000	Enhancers	Psoas Muscle	Psoas
15	chr6:150209600-150215800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:150209600-150216000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:150209600-150222200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:150210000-150211600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:150210200-150211400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:150210200-150211800	Weak transcription	Esophagus	oesophagus
21	chr6:150210400-150210800	Genic enhancers	HMEC	breast
22	chr6:150210400-150211400	Weak transcription	HSMM	muscle
23	chr6:150210400-150211400	Genic enhancers	NHEK	skin
24	chr6:150210400-150211600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:150210400-150211600	Weak transcription	Osteobl	bone
26	chr6:150210400-150211800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:150210600-150211000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:150210600-150211600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:150210600-150211600	Weak transcription	NHDF-Ad	bronchial
30	chr6:150210600-150212800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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