Variant report

Variant	rs2076470
Chromosome Location	chr6:2434522-2434523
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	JUND	chr6:2434160-2434858	HCT-116	colon:	n/a	n/a
2	TEAD4	chr6:2433675-2435640	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr6:2434361-2434704	MCF10A-Er-Src	breast:	n/a	n/a
4	TCF12	chr6:2433745-2435613	ECC-1	luminal epithelium:	n/a	chr6:2435355-2435363 chr6:2434823-2434830
5	SP1	chr6:2434075-2435027	HCT-116	colon:	n/a	chr6:2434258-2434268
6	FOSL1	chr6:2434100-2434894	HCT-116	colon:	n/a	n/a
7	NFIC	chr6:2433722-2434981	ECC-1	luminal epithelium:	n/a	n/a
8	NR2F2	chr6:2434252-2434851	MCF-7	breast:	n/a	n/a
9	NFIC	chr6:2433647-2436143	ECC-1	luminal epithelium:	n/a	n/a
10	FOS	chr6:2434363-2434701	MCF10A-Er-Src	breast:	n/a	n/a
11	YY1	chr6:2434319-2434908	ECC-1	luminal epithelium:	n/a	chr6:2434650-2434661
12	EP300	chr6:2433736-2434882	ECC-1	luminal epithelium:	n/a	chr6:2434486-2434493
13	SP1	chr6:2433976-2434988	HCT-116	colon:	n/a	chr6:2434258-2434268
14	FOS	chr6:2434363-2434687	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr6:2434385-2434698	MCF10A-Er-Src	breast:	n/a	n/a
16	CBX3	chr6:2433971-2434832	HCT-116	colon:	n/a	n/a
17	USF1	chr6:2434251-2435051	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr6:2433839-2434942	ECC-1	luminal epithelium:	n/a	n/a
19	STAT3	chr6:2434451-2434660	MCF10A-Er-Src	breast:	n/a	n/a
20	ESR1	chr6:2434280-2434778	ECC-1	luminal epithelium:	n/a	n/a
21	TEAD4	chr6:2433713-2434945	ECC-1	luminal epithelium:	n/a	n/a
22	ESR1	chr6:2433767-2434817	ECC-1	luminal epithelium:	n/a	n/a
23	YY1	chr6:2433795-2434928	ECC-1	luminal epithelium:	n/a	chr6:2434650-2434661
24	YY1	chr6:2434402-2434716	HCT-116	colon:	n/a	chr6:2434650-2434661
25	USF1	chr6:2434379-2435069	ECC-1	luminal epithelium:	n/a	n/a
26	MYC	chr6:2434446-2434630	MCF-7	breast:	n/a	n/a
27	MAX	chr6:2433848-2435486	ECC-1	luminal epithelium:	n/a	chr6:2434783-2434792 chr6:2434782-2434791 chr6:2434782-2434791 chr6:2434777-2434796
28	ESR1	chr6:2434428-2434663	ECC-1	luminal epithelium:	n/a	n/a
29	ELF1	chr6:2434195-2434825	MCF-7	breast:	n/a	n/a
30	POLR2A	chr6:2434366-2434681	HCT-116	colon:	n/a	n/a
31	POLR2A	chr6:2434513-2434543	MCF-7	breast:	n/a	n/a
32	POLR2A	chr6:2434484-2434896	ECC-1	luminal epithelium:	n/a	n/a
33	TCF12	chr6:2433625-2435000	ECC-1	luminal epithelium:	n/a	chr6:2434823-2434830
34	EP300	chr6:2433679-2435728	ECC-1	luminal epithelium:	n/a	chr6:2434486-2434493
35	ESR1	chr6:2433886-2434729	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr6:2434330-2434619	HCT-116	colon:	n/a	n/a
37	MAX	chr6:2433773-2434538	NB4	blood:	n/a	n/a
38	MYC	chr6:2434453-2434588	MCF10A-Er-Src	breast:	n/a	n/a
39	MAX	chr6:2433831-2435027	ECC-1	luminal epithelium:	n/a	chr6:2434783-2434792 chr6:2434782-2434791 chr6:2434782-2434791 chr6:2434777-2434796
40	FOSL1	chr6:2434196-2434867	HCT-116	colon:	n/a	n/a
41	MYC	chr6:2434467-2434653	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000272465	TF binding region

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10458063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10458138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10458139	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10458140	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10458141	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10458142	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11242769	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242770	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242772	0.93[EUR][1000 genomes]
rs11242773	0.86[EUR][1000 genomes]
rs11242775	0.83[EUR][1000 genomes]
rs11753825	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11758482	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12189681	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12189724	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12195877	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12196223	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12199363	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12199637	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12205452	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206851	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12209220	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12209322	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12209326	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12210286	0.83[EUR][1000 genomes]
rs12210452	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12213643	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12528202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662045	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13214565	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13220392	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2073003	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294659	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34885387	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35144026	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3734506	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3817904	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9328099	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs982096	0.90[EUR][1000 genomes]
rs983027	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs983028	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2399800-2449200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:2402200-2449200	Weak transcription	Left Ventricle	heart
3	chr6:2414600-2434600	Weak transcription	Fetal Intestine Small	intestine
4	chr6:2414600-2452000	Weak transcription	Ovary	ovary
5	chr6:2414800-2448800	Weak transcription	Liver	Liver
6	chr6:2414800-2449200	Weak transcription	Fetal Stomach	stomach
7	chr6:2417600-2454200	Weak transcription	Pancreas	Pancrea
8	chr6:2426400-2439800	Weak transcription	Aorta	Aorta
9	chr6:2428800-2446200	Weak transcription	Right Ventricle	heart
10	chr6:2431000-2434800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:2431200-2434800	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:2431400-2435400	Enhancers	HMEC	breast
13	chr6:2431600-2439800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:2431800-2435800	Enhancers	Esophagus	oesophagus
15	chr6:2432000-2435000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:2432000-2435200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr6:2432200-2435000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:2432200-2435000	Enhancers	NHEK	skin
19	chr6:2432200-2435400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:2432200-2449200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:2432400-2435000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:2432800-2434800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:2433000-2434800	Enhancers	Fetal Thymus	thymus
24	chr6:2433200-2449200	Weak transcription	Adipose Nuclei	Adipose
25	chr6:2433400-2437200	Weak transcription	HSMM	muscle
26	chr6:2433600-2434600	Enhancers	Spleen	Spleen
27	chr6:2433600-2447000	Weak transcription	Fetal Intestine Large	intestine
28	chr6:2433800-2434600	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:2433800-2435000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:2434000-2434600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr6:2434000-2434800	Enhancers	Placenta	Placenta
32	chr6:2434000-2435000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:2434000-2437000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:2434000-2437600	Enhancers	Fetal Kidney	kidney
35	chr6:2434000-2448400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:2434200-2434600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr6:2434200-2434800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:2434200-2435000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr6:2434200-2442600	Weak transcription	Lung	lung
40	chr6:2434400-2435000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:2434400-2435200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:2434400-2449200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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