Variant report

Variant	rs9392588
Chromosome Location	chr6:4350992-4350993
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	USF2	chr6:4350735-4351301	Hela-S3	cervix:	n/a	n/a
2	CHD2	chr6:4350774-4351386	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr6:4350759-4351204	Hela-S3	cervix:	n/a	n/a
4	GATA2	chr6:4350747-4351256	HUVEC	blood vessel:	n/a	n/a
5	NFYB	chr6:4350760-4351281	Hela-S3	cervix:	n/a	chr6:4350931-4350941 chr6:4350926-4350941
6	STAT3	chr6:4350875-4351227	MCF10A-Er-Src	breast:	n/a	n/a
7	BRCA1	chr6:4350805-4351110	Hela-S3	cervix:	n/a	n/a
8	FOS	chr6:4350885-4351291	MCF10A-Er-Src	breast:	n/a	n/a
9	REST	chr6:4350906-4351396	PFSK-1	brain:	n/a	chr6:4351264-4351273
10	FOS	chr6:4350820-4351216	HUVEC	blood vessel:	n/a	n/a
11	REST	chr6:4350872-4351490	PFSK-1	brain:	n/a	chr6:4351264-4351273
12	EP300	chr6:4350772-4351215	Hela-S3	cervix:	n/a	n/a
13	SMC3	chr6:4350771-4351273	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr6:4350743-4351229	Hela-S3	cervix:	n/a	n/a
15	MAFK	chr6:4350892-4351088	Hela-S3	cervix:	n/a	n/a
16	MXI1	chr6:4350823-4351023	Hela-S3	cervix:	n/a	n/a
17	GTF2F1	chr6:4350759-4351457	Hela-S3	cervix:	n/a	n/a
18	REST	chr6:4350963-4351527	ECC-1	luminal epithelium:	n/a	chr6:4351264-4351273
19	FOS	chr6:4350888-4351175	MCF10A-Er-Src	breast:	n/a	n/a
20	PRDM1	chr6:4350876-4351051	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr6:4350828-4351177	HUVEC	blood vessel:	n/a	n/a
22	TCF7L2	chr6:4350814-4351183	Hela-S3	cervix:	n/a	n/a
23	MAZ	chr6:4350878-4351081	Hela-S3	cervix:	n/a	n/a
24	ELK4	chr6:4350951-4351255	Hela-S3	cervix:	n/a	chr6:4351042-4351053
25	NFIC	chr6:4350746-4351360	SK-N-SH	brain:	n/a	n/a
26	JUN	chr6:4350792-4353337	K562	blood:	n/a	chr6:4352481-4352488 chr6:4352481-4352489 chr6:4352479-4352491 chr6:4352480-4352489
27	POLR2A	chr6:4350775-4351246	HUVEC	blood vessel:	n/a	n/a
28	RCOR1	chr6:4350756-4351188	Hela-S3	cervix:	n/a	n/a
29	FOS	chr6:4350980-4351172	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr6:4350790-4351214	MCF10A-Er-Src	breast:	n/a	n/a
31	MYC	chr6:4350967-4351167	HUVEC	blood vessel:	n/a	n/a
32	STAT3	chr6:4350847-4351249	MCF10A-Er-Src	breast:	n/a	n/a
33	MAX	chr6:4350751-4351176	Hela-S3	cervix:	n/a	n/a
34	CEBPB	chr6:4350829-4351135	Hela-S3	cervix:	n/a	n/a
35	RFX5	chr6:4350793-4351191	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr6:4350927-4351125	MCF10A-Er-Src	breast:	n/a	n/a
37	NFYA	chr6:4350809-4351453	Hela-S3	cervix:	n/a	chr6:4350931-4350941

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4349515..4351510-chr6:4353133..4355673,2	MCF-7	breast:
2	chr6:4321843..4323529-chr6:4350636..4352389,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231811	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs4959277	0.95[CEU][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4959279	0.95[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs4959940	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4959941	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4959943	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4959945	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6901775	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs746360	0.85[ASN][1000 genomes]
rs7740780	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs914044	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328246	0.82[ASN][1000 genomes]
rs9378399	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9378862	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9378863	0.95[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9392038	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9392040	0.80[ASN][1000 genomes]
rs9392582	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9392589	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9405724	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv600861	chr6:4238488-4469641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv462618	chr6:4238488-4472587	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv600862	chr6:4238488-4472587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv949364	chr6:4253413-4466981	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv600863	chr6:4255387-4472587	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1027498	chr6:4255640-4471635	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv2763995	chr6:4255640-4474114	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1020205	chr6:4255640-4474114	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv600864	chr6:4255708-4464630	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv516402	chr6:4255708-4472587	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv462619	chr6:4255708-4472587	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv600865	chr6:4255708-4472587	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv462620	chr6:4255708-4481421	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv600866	chr6:4255708-4481421	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv600867	chr6:4255725-4464630	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv462621	chr6:4255725-4472587	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv600868	chr6:4255725-4472587	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv1029501	chr6:4255745-4471635	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv432845	chr6:4255905-4471472	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv1030655	chr6:4257190-4473701	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv538108	chr6:4257190-4473701	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv1030840	chr6:4257390-4473562	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv538109	chr6:4257390-4473562	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
25	nsv1026890	chr6:4259075-4471635	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv1030588	chr6:4264933-4455210	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
27	nsv1021257	chr6:4264933-4473384	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
28	nsv538110	chr6:4264933-4473384	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
29	nsv916553	chr6:4269714-4437920	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
30	nsv1016621	chr6:4277411-4473384	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
31	nsv600869	chr6:4294450-4430623	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
32	nsv883412	chr6:4349808-4376376	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4345000-4351600	Weak transcription	HSMMtube	muscle
2	chr6:4345200-4351400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:4345800-4353600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:4347200-4351800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:4347400-4358600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:4347600-4351800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:4347600-4351800	Enhancers	NHLF	lung
8	chr6:4348000-4351200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:4348000-4351800	Weak transcription	HSMM	muscle
10	chr6:4348200-4351400	Weak transcription	Right Ventricle	heart
11	chr6:4348200-4352000	Enhancers	Rectal Smooth Muscle	rectum
12	chr6:4348400-4351600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:4349000-4351000	Weak transcription	NH-A	brain
14	chr6:4349000-4351600	Weak transcription	Fetal Heart	heart
15	chr6:4349000-4351800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:4349600-4351600	Enhancers	NHDF-Ad	bronchial
17	chr6:4349800-4351000	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:4349800-4351400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:4349800-4351800	Enhancers	Right Atrium	heart
20	chr6:4350000-4351800	Enhancers	Hela-S3	cervix
21	chr6:4350000-4351800	Enhancers	HMEC	breast
22	chr6:4350200-4351200	Enhancers	Lung	lung
23	chr6:4350200-4351400	Enhancers	Fetal Muscle Trunk	muscle
24	chr6:4350200-4352000	Enhancers	Fetal Muscle Leg	muscle
25	chr6:4350200-4352800	Enhancers	HUVEC	blood vessel
26	chr6:4350200-4353200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:4350400-4351600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:4350400-4351800	Enhancers	Adipose Nuclei	Adipose
29	chr6:4350400-4352000	Enhancers	Left Ventricle	heart
30	chr6:4350400-4352800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:4350400-4353600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:4350600-4351000	Enhancers	Stomach Smooth Muscle	stomach
33	chr6:4350600-4351400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:4350600-4351800	Enhancers	Brain Cingulate Gyrus	brain
35	chr6:4350600-4351800	Enhancers	Brain Hippocampus Middle	brain
36	chr6:4350600-4351800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:4350600-4351800	Enhancers	NHEK	skin
38	chr6:4350600-4352000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:4350600-4353200	Enhancers	Fetal Stomach	stomach
40	chr6:4350600-4353400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:4350600-4358800	Weak transcription	Spleen	Spleen
42	chr6:4350800-4351000	Enhancers	Placenta	Placenta
43	chr6:4350800-4351000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr6:4350800-4351200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:4350800-4351200	Enhancers	Brain Substantia Nigra	brain
46	chr6:4350800-4351600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr6:4350800-4351600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr6:4350800-4351800	Bivalent Enhancer	Fetal Lung	lung
49	chr6:4350800-4351800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr6:4350800-4351800	Enhancers	Osteobl	bone

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