Variant report

Variant	rs71570854
Chromosome Location	chr6:117762250-117762251
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	MAX	chr6:117761896-117762662	Hela-S3	cervix:	n/a	n/a
2	RXRA	chr6:117762009-117762890	SK-N-SH	brain:	n/a	chr6:117762519-117762528
3	BRCA1	chr6:117761605-117762791	Hela-S3	cervix:	n/a	n/a
4	NFIC	chr6:117762083-117762776	SK-N-SH	brain:	n/a	n/a
5	REST	chr6:117761898-117762800	A549	lung:	n/a	n/a
6	TAF1	chr6:117762249-117762697	SK-N-SH	brain:	n/a	n/a
7	NR3C1	chr6:117761834-117762757	A549	lung:	n/a	n/a
8	RCOR1	chr6:117761772-117762923	IMR90	lung:	n/a	n/a
9	SP1	chr6:117761688-117763617	A549	lung:	n/a	n/a
10	POLR2A	chr6:117762122-117762787	U87	brain:	n/a	n/a
11	PBX3	chr6:117761838-117762830	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr6:117761585-117763733	A549	lung:	n/a	n/a
13	JUND	chr6:117761733-117762949	SK-N-SH	brain:	n/a	n/a
14	STAT3	chr6:117761798-117762768	MCF10A-Er-Src	breast:	n/a	chr6:117762443-117762451
15	CEBPB	chr6:117761806-117762772	A549	lung:	n/a	chr6:117762474-117762485 chr6:117762474-117762485
16	FOXA2	chr6:117761856-117762889	A549	lung:	n/a	n/a
17	TCF12	chr6:117761687-117763150	SK-N-SH	brain:	n/a	n/a
18	YY1	chr6:117762054-117762798	SK-N-SH	brain:	n/a	n/a
19	TEAD4	chr6:117762017-117762979	SK-N-SH	brain:	n/a	n/a
20	GATA3	chr6:117761855-117762768	A549	lung:	n/a	n/a
21	SP1	chr6:117761729-117762842	A549	lung:	n/a	n/a
22	TEAD4	chr6:117762105-117762721	A549	lung:	n/a	n/a
23	STAT3	chr6:117761880-117762815	MCF10A-Er-Src	breast:	n/a	chr6:117762443-117762451
24	MAX	chr6:117762114-117762811	SK-N-SH	brain:	n/a	n/a
25	ATF3	chr6:117762158-117762748	A549	lung:	n/a	n/a
26	EP300	chr6:117761855-117763033	SK-N-SH	brain:	n/a	n/a
27	GATA3	chr6:117761550-117763737	A549	lung:	n/a	chr6:117762884-117762893
28	FOXM1	chr6:117762080-117762759	SK-N-SH	brain:	n/a	n/a
29	EP300	chr6:117761608-117763725	A549	lung:	n/a	chr6:117763160-117763174
30	ATF3	chr6:117762073-117762812	A549	lung:	n/a	n/a
31	TCF7L2	chr6:117761806-117762703	Hela-S3	cervix:	n/a	n/a
32	EP300	chr6:117761674-117763448	Hela-S3	cervix:	n/a	chr6:117763160-117763174
33	FOSL2	chr6:117762085-117762825	SK-N-SH	brain:	n/a	n/a
34	TBP	chr6:117761697-117762762	Hela-S3	cervix:	n/a	n/a
35	EP300	chr6:117762200-117762717	SK-N-SH_RA	brain:	n/a	n/a
36	NR3C1	chr6:117762226-117762359	A549	lung:	n/a	n/a
37	CEBPB	chr6:117762057-117762584	HCT-116	colon:	n/a	chr6:117762474-117762485 chr6:117762474-117762485
38	STAT3	chr6:117761784-117762744	MCF10A-Er-Src	breast:	n/a	chr6:117762443-117762451
39	MXI1	chr6:117761792-117762637	Hela-S3	cervix:	n/a	n/a
40	FOS	chr6:117761773-117762737	MCF10A-Er-Src	breast:	n/a	n/a
41	USF2	chr6:117761929-117762655	Hela-S3	cervix:	n/a	n/a
42	JUND	chr6:117761713-117762946	SK-N-SH	brain:	n/a	n/a
43	NFYB	chr6:117761903-117762639	Hela-S3	cervix:	n/a	chr6:117762065-117762080
44	GTF2F1	chr6:117761699-117762764	Hela-S3	cervix:	n/a	n/a
45	STAT3	chr6:117761688-117762763	MCF10A-Er-Src	breast:	n/a	chr6:117762443-117762451
46	EP300	chr6:117761831-117762785	SK-N-SH_RA	brain:	n/a	n/a
47	POLR2A	chr6:117762115-117762758	SK-N-SH	brain:	n/a	n/a
48	CHD2	chr6:117761787-117762755	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr6:117761449-117762789	U87	brain:	n/a	n/a
50	FOSL2	chr6:117761770-117762830	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000221434	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10484302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12332810	0.84[ASN][1000 genomes]
rs13194436	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13196657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13197031	0.84[ASN][1000 genomes]
rs13199989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13202073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13205893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206903	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211770	0.92[ASN][1000 genomes]
rs13212301	0.84[ASN][1000 genomes]
rs13212382	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1358850	0.92[ASN][1000 genomes]
rs17079150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17090953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1853149	0.84[ASN][1000 genomes]
rs2243375	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2243377	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2273603	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34059111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34231660	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34258179	0.80[AMR][1000 genomes]
rs34280338	0.80[AMR][1000 genomes]
rs34900812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34959842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35476086	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35562167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35837924	0.84[EUR][1000 genomes]
rs35874725	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35917072	0.82[EUR][1000 genomes]
rs35921544	0.84[ASN][1000 genomes]
rs36111427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36122926	0.84[ASN][1000 genomes]
rs3798391	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3798392	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67157504	0.92[ASN][1000 genomes]
rs71554882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71570849	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71570850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71570852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72969418	0.84[ASN][1000 genomes]
rs9372479	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9481709	0.84[ASN][1000 genomes]
rs9489153	0.84[ASN][1000 genomes]
rs9489162	0.84[ASN][1000 genomes]
rs9489163	0.84[ASN][1000 genomes]
rs9489165	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv966655	chr6:117758375-117766294	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117760000-117762600	Enhancers	HMEC	breast
2	chr6:117761000-117762600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:117761200-117762800	Weak transcription	HSMM	muscle
4	chr6:117761200-117763400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:117761600-117762800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:117761600-117762800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:117761600-117763800	Enhancers	NHEK	skin
8	chr6:117761800-117763400	Enhancers	NHDF-Ad	bronchial
9	chr6:117761800-117763600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:117762000-117762400	Weak transcription	Hela-S3	cervix
11	chr6:117762000-117762800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:117762000-117763400	Enhancers	NH-A	brain
13	chr6:117762000-117763400	Enhancers	NHLF	lung
14	chr6:117762000-117763800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:117762000-117764600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:117762000-117767800	Enhancers	Osteobl	bone
17	chr6:117762200-117762400	Enhancers	A549	lung
18	chr6:117762200-117762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:117762200-117763400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:117762200-117763400	Enhancers	HSMMtube	muscle

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