Variant report

Variant	rs6858700
Chromosome Location	chr4:100576651-100576652
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	E2F6	chr4:100576516-100576932	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr4:100576608-100576787	MCF10A-Er-Src	breast:	n/a	n/a
3	MAX	chr4:100576524-100576895	ECC-1	luminal epithelium:	n/a	chr4:100576740-100576749
4	FOS	chr4:100576371-100576873	MCF10A-Er-Src	breast:	n/a	chr4:100576382-100576390 chr4:100576381-100576391 chr4:100576383-100576394 chr4:100576381-100576391
5	MAX	chr4:100576464-100576954	Hela-S3	cervix:	n/a	chr4:100576740-100576749
6	NFIC	chr4:100576293-100577023	ECC-1	luminal epithelium:	n/a	n/a
7	FOS	chr4:100576377-100576881	MCF10A-Er-Src	breast:	n/a	chr4:100576382-100576390 chr4:100576381-100576391 chr4:100576383-100576394 chr4:100576381-100576391
8	CEBPB	chr4:100576490-100576945	Hela-S3	cervix:	n/a	chr4:100576805-100576816 chr4:100576805-100576818
9	GTF2F1	chr4:100576564-100576871	Hela-S3	cervix:	n/a	n/a
10	E2F4	chr4:100576542-100576866	MCF10A-Er-Src	breast:	n/a	n/a
11	SMC3	chr4:100576464-100576880	Hela-S3	cervix:	n/a	n/a
12	CHD2	chr4:100576458-100576934	Hela-S3	cervix:	n/a	n/a
13	TCF7L2	chr4:100576510-100577029	Hela-S3	cervix:	n/a	n/a
14	TFAP2A	chr4:100576366-100576992	Hela-S3	cervix:	n/a	chr4:100576626-100576638
15	MAX	chr4:100576466-100576898	Hela-S3	cervix:	n/a	chr4:100576740-100576749
16	MAX	chr4:100576465-100576896	ECC-1	luminal epithelium:	n/a	chr4:100576740-100576749
17	FOS	chr4:100576459-100576853	MCF10A-Er-Src	breast:	n/a	n/a
18	NR2F2	chr4:100576406-100577025	MCF-7	breast:	n/a	n/a
19	RFX5	chr4:100576516-100576839	Hela-S3	cervix:	n/a	n/a
20	MYC	chr4:100576446-100576867	MCF10A-Er-Src	breast:	n/a	chr4:100576740-100576749
21	EP300	chr4:100576413-100576878	Hela-S3	cervix:	n/a	chr4:100576711-100576725
22	STAT3	chr4:100576480-100576860	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr4:100576472-100576785	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr4:100576578-100576807	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr4:100576371-100576873	MCF10A-Er-Src	breast:	n/a	chr4:100576740-100576749
26	STAT3	chr4:100576544-100576873	MCF10A-Er-Src	breast:	n/a	n/a
27	TFAP2C	chr4:100576366-100577041	Hela-S3	cervix:	n/a	chr4:100576623-100576638
28	STAT3	chr4:100576470-100576866	MCF10A-Er-Src	breast:	n/a	n/a
29	MAX	chr4:100576456-100576933	MCF-7	breast:	n/a	chr4:100576740-100576749

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:100576610-100576660	NHDF-neo	bronchial:	n/a
2	chr4:100576610-100576660	AG04449	skin:	fetal
3	chr4:100576610-100576660	HPAEpiC	pulmonary alveolar:	n/a
4	chr4:100576610-100576660	IMR90	lung:	fetal
5	chr4:100576610-100576660	PrEC	prostate:	n/a
6	chr4:100576610-100576660	MCF-7	breast:	n/a
7	chr4:100576610-100576660	PFSK-1	brain:	n/a
8	chr4:100576610-100576660	Hepatocyte	liver:	n/a
9	chr4:100576610-100576660	ovcar-3	ovarian:	n/a
10	chr4:100576610-100576660	HL-60	blood:	n/a
11	chr4:100576610-100576660	HCPEpiC	choroid plexus:	n/a
12	chr4:100576610-100576660	HRCEpiC	kidney:	n/a
13	chr4:100576610-100576660	BJ	skin:	n/a
14	chr4:100576610-100576660	GM19239	blood:	n/a
15	chr4:100576610-100576660	HIPEpiC	eye:	n/a
16	chr4:100576610-100576660	K562	blood:	n/a
17	chr4:100576610-100576660	HEEpiC	esophagus:	n/a
18	chr4:100576610-100576660	AoSMC	blood vessel:	n/a
19	chr4:100576610-100576660	MCF10A-Er-Src	breast:	n/a
20	chr4:100576610-100576660	HAEpiC	amniotic membrane:	n/a
21	chr4:100576610-100576660	SK-N-MC	brain:	n/a
22	chr4:100576610-100576660	NT2-D1	testis:	n/a
23	chr4:100576610-100576660	HCT-116	colon:	n/a
24	chr4:100576610-100576660	HNPCEpiC	eye:	n/a
25	chr4:100576610-100576660	GM06990	blood:	n/a
26	chr4:100576610-100576660	LNCaP	prostate:	n/a
27	chr4:100576610-100576660	SKMC	muscle:	n/a
28	chr4:100576610-100576660	SK-N-SH	brain:	n/a
29	chr4:100576610-100576660	AG10803	skin:	n/a
30	chr4:100576610-100576660	H1-hESC	embryonic stem cell:	embryo
31	chr4:100576610-100576660	NH-A	brain:	n/a
32	chr4:100576610-100576660	HMEC	breast:	n/a
33	chr4:100576610-100576660	A549	lung:	n/a
34	chr4:100576610-100576660	Caco-2	colon:	n/a
35	chr4:100576610-100576660	SK-N-SH_RA	brain:	n/a
36	chr4:100576610-100576660	T-47D	breast:	n/a
37	chr4:100576610-100576660	GM12891	blood:	n/a
38	chr4:100576610-100576660	RPTEC	kidney:	n/a
39	chr4:100576610-100576660	AG09319	gingival:	n/a
40	chr4:100576610-100576660	ProgFib	skin:	n/a
41	chr4:100576610-100576660	GM12878	blood:	n/a
42	chr4:100576610-100576660	HEK293	kidney:	embryo
43	chr4:100576610-100576660	NB4	blood:	n/a
44	chr4:100576610-100576660	AG09309	skin:	n/a
45	chr4:100576610-100576660	HCM	heart:	n/a
46	chr4:100576610-100576660	GM12892	blood:	n/a
47	chr4:100576610-100576660	BE2_C	brain:	n/a
48	chr4:100576610-100576660	HUVEC	blood vessel:	n/a
49	chr4:100576610-100576660	SAEC	small airway:	n/a
50	chr4:100576610-100576660	Hela-S3	cervix:	n/a

Variant related genes	Relation type
ENSG00000248713	TF binding region
ENSG00000248713	CpG island

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10516446	0.88[ASN][1000 genomes]
rs11097667	0.82[ASN][1000 genomes]
rs11097669	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12643429	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12647527	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12648918	0.87[ASN][1000 genomes]
rs1352777	0.87[ASN][1000 genomes]
rs1491242	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17029135	0.82[ASN][1000 genomes]
rs17029142	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs17029165	0.87[ASN][1000 genomes]
rs17029251	0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17029277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17029292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298747	0.86[ASN][1000 genomes]
rs2306984	0.87[ASN][1000 genomes]
rs3792681	0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3828542	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4235440	0.87[ASN][1000 genomes]
rs4699384	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4699385	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699754	0.82[ASN][1000 genomes]
rs4699756	0.87[ASN][1000 genomes]
rs61074475	0.87[ASN][1000 genomes]
rs6817049	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72906793	0.82[ASN][1000 genomes]
rs72908710	0.87[ASN][1000 genomes]
rs72908716	0.87[ASN][1000 genomes]
rs72908742	0.96[ASN][1000 genomes]
rs871321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs881980	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs931465	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs956200	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933074	chr4:100460951-100630600	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100567800-100579200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:100575000-100577200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:100575200-100577200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:100575400-100576800	Enhancers	Fetal Brain Male	brain
5	chr4:100575800-100576800	Weak transcription	Left Ventricle	heart
6	chr4:100575800-100577000	Enhancers	Rectal Smooth Muscle	rectum
7	chr4:100575800-100577600	Enhancers	Hela-S3	cervix
8	chr4:100575800-100579800	Weak transcription	Right Atrium	heart
9	chr4:100576000-100577000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:100576000-100577000	Enhancers	HSMM	muscle
11	chr4:100576000-100577200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:100576000-100579400	Weak transcription	Psoas Muscle	Psoas
13	chr4:100576200-100577000	Enhancers	Brain Anterior Caudate	brain
14	chr4:100576200-100577000	Enhancers	NH-A	brain
15	chr4:100576200-100577200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr4:100576200-100577200	Enhancers	HMEC	breast
17	chr4:100576400-100576800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:100576400-100576800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:100576400-100576800	Flanking Active TSS	Fetal Lung	lung
20	chr4:100576400-100576800	Enhancers	Fetal Stomach	stomach
21	chr4:100576400-100577000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:100576400-100577000	Enhancers	Aorta	Aorta
23	chr4:100576400-100577000	Flanking Active TSS	HSMMtube	muscle
24	chr4:100576400-100577200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:100576400-100577200	Enhancers	Colon Smooth Muscle	Colon
26	chr4:100576400-100577200	Enhancers	Ovary	ovary
27	chr4:100576400-100577200	Enhancers	NHEK	skin
28	chr4:100576400-100577400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:100576400-100577800	Enhancers	Fetal Muscle Trunk	muscle
30	chr4:100576600-100577000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr4:100576600-100577000	Enhancers	Brain Angular Gyrus	brain
32	chr4:100576600-100577000	Flanking Active TSS	Right Ventricle	heart
33	chr4:100576600-100577200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:100576600-100577400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr4:100576600-100577600	Enhancers	Fetal Heart	heart
36	chr4:100576600-100578600	Enhancers	Fetal Muscle Leg	muscle

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