Variant report

Variant	rs6808866
Chromosome Location	chr3:179066282-179066283
allele	C/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	TEAD4	chr3:179065149-179066452	K562	blood:	n/a	n/a
2	POLR2A	chr3:179065161-179066569	GM12891	blood:	n/a	n/a
3	PML	chr3:179064948-179066566	GM12878	blood:	n/a	n/a
4	MXI1	chr3:179065241-179066505	Hela-S3	cervix:	n/a	n/a
5	MYC	chr3:179065256-179066452	K562	blood:	n/a	chr3:179065500-179065510
6	WRNIP1	chr3:179065955-179066796	GM12878	blood:	n/a	n/a
7	CHD2	chr3:179065208-179066487	GM12878	blood:	n/a	n/a
8	CHD1	chr3:179065141-179066765	GM12878	blood:	n/a	n/a
9	EP300	chr3:179066123-179066478	GM12878	blood:	n/a	chr3:179066212-179066226
10	POLR2A	chr3:179065109-179066721	Raji	blood:	n/a	n/a
11	STAT5A	chr3:179065128-179066518	GM12878	blood:	n/a	chr3:179065844-179065856 chr3:179065320-179065332
12	BCL3	chr3:179066095-179066512	GM12878	blood:	n/a	n/a
13	CUX1	chr3:179065830-179066692	GM12878	blood:	n/a	n/a
14	PAX5	chr3:179065152-179066488	GM12891	blood:	n/a	chr3:179066299-179066318
15	MTA3	chr3:179064793-179066809	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:179065155-179066460	GM12891	blood:	n/a	n/a
17	ATF2	chr3:179065849-179066591	GM12878	blood:	n/a	n/a
18	FOS	chr3:179066280-179066476	MCF10A-Er-Src	breast:	n/a	n/a
19	TAF1	chr3:179066059-179066371	GM12891	blood:	n/a	n/a
20	MXI1	chr3:179065305-179066705	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:179065159-179066545	GM12892	blood:	n/a	n/a
22	PAX5	chr3:179065153-179066571	GM12878	blood:	n/a	chr3:179066299-179066318
23	SP1	chr3:179066095-179066484	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:179064886-179066769	GM18505	blood:	n/a	n/a
25	RELA	chr3:179065185-179066664	GM19099	blood:	n/a	n/a
26	FOXM1	chr3:179065832-179066756	GM12878	blood:	n/a	n/a
27	STAT5A	chr3:179065879-179066493	GM12878	blood:	n/a	n/a
28	HCFC1	chr3:179064891-179066842	Hela-S3	cervix:	n/a	n/a
29	ELF1	chr3:179065146-179066403	GM12878	blood:	n/a	chr3:179065470-179065483 chr3:179065663-179065675 chr3:179065432-179065441 chr3:179065431-179065444
30	MEF2A	chr3:179065975-179066566	GM12878	blood:	n/a	chr3:179066214-179066222
31	POLR2A	chr3:179065170-179067141	GM12878	blood:	n/a	n/a
32	MYC	chr3:179065192-179066644	K562	blood:	n/a	chr3:179065500-179065510
33	POLR2A	chr3:179064094-179066784	GM12891	blood:	n/a	n/a
34	PAX5	chr3:179066016-179066445	GM12878	blood:	n/a	chr3:179066299-179066318
35	POLR2A	chr3:179065153-179066387	GM12892	blood:	n/a	n/a
36	MAZ	chr3:179065160-179066589	GM12878	blood:	n/a	chr3:179065500-179065510
37	POLR2A	chr3:179064886-179066317	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr3:179065148-179066370	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:179065163-179066724	GM12878	blood:	n/a	n/a
40	NFATC1	chr3:179065965-179066763	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:179065120-179066845	GM19099	blood:	n/a	n/a
42	POLR2A	chr3:179065207-179066540	GM12878	blood:	n/a	n/a
43	STAT1	chr3:179066000-179066466	GM12878	blood:	n/a	n/a
44	CTCF	chr3:179066241-179066382	Spleen_OC	spleen:	n/a	n/a
45	MAX	chr3:179065166-179066608	ECC-1	luminal epithelium:	n/a	chr3:179065500-179065510
46	RELA	chr3:179065144-179066636	GM18951	blood:	n/a	n/a
47	STAT3	chr3:179066040-179066749	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:179065158-179066751	GM12891	blood:	n/a	n/a
49	GTF2F1	chr3:179065345-179066295	K562	blood:	n/a	n/a
50	POLR2A	chr3:179064747-179066709	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:179065009..179066943-chr3:179078070..179080733,2	K562	blood:
2	chr3:179039334..179043117-chr3:179061578..179071936,16	MCF-7	breast:
3	chr3:179062884..179066516-chr3:179279392..179283320,5	K562	blood:
4	chr3:179064557..179067034-chr3:179115322..179117988,2	MCF-7	breast:
5	chr16:4233214..4233861-chr3:179065342..179066324,2	Hela-S3	cervix:
6	chr3:179063838..179066998-chr3:179279826..179282991,3	K562	blood:
7	chr3:179040254..179044115-chr3:179063916..179068626,6	K562	blood:
8	chr3:178787639..178789990-chr3:179064273..179066880,2	MCF-7	breast:
9	chr3:178864465..178866059-chr3:179064181..179066320,2	K562	blood:
10	chr3:179039679..179043417-chr3:179063023..179066951,5	K562	blood:
11	chr3:179064036..179066724-chr3:179094064..179095698,2	MCF-7	breast:
12	chr3:179040252..179043387-chr3:179064355..179067344,4	MCF-7	breast:
13	chr3:179064139..179066527-chr3:179074773..179078011,3	MCF-7	breast:
14	chr3:178788594..178790647-chr3:179063924..179066564,2	K562	blood:

Variant related genes	Relation type
MFN1	TF binding region
ENSG00000242539	Chromatin interaction
ENSG00000269728	Chromatin interaction
ENSG00000263105	Chromatin interaction
ENSG00000121879	Chromatin interaction
ENSG00000136518	Chromatin interaction
ENSG00000121864	Chromatin interaction
ENSG00000229102	Chromatin interaction
ENSG00000171109	Chromatin interaction
ENSG00000172667	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11916825	1.00[AMR][1000 genomes]
rs11919840	1.00[AMR][1000 genomes]
rs11925064	1.00[AMR][1000 genomes]
rs11925248	1.00[AMR][1000 genomes]
rs11927084	1.00[AMR][1000 genomes]
rs13317510	0.89[AMR][1000 genomes]
rs16830445	0.89[AMR][1000 genomes]
rs16830460	0.89[AMR][1000 genomes]
rs28512433	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28522651	1.00[AMR][1000 genomes]
rs55805052	1.00[AMR][1000 genomes]
rs56210820	0.89[AMR][1000 genomes]
rs56265474	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56280435	1.00[AMR][1000 genomes]
rs57148977	1.00[AMR][1000 genomes]
rs57526364	1.00[AMR][1000 genomes]
rs57795346	1.00[AMR][1000 genomes]
rs58741861	0.89[AMR][1000 genomes]
rs59062224	1.00[AMR][1000 genomes]
rs59333548	0.89[AMR][1000 genomes]
rs59511701	1.00[AMR][1000 genomes]
rs59564372	1.00[AMR][1000 genomes]
rs60191176	1.00[AMR][1000 genomes]
rs60746059	1.00[AMR][1000 genomes]
rs61246771	0.89[AMR][1000 genomes]
rs61325843	1.00[AMR][1000 genomes]
rs6778235	0.89[AMR][1000 genomes]
rs6800044	0.89[AMR][1000 genomes]
rs6808033	0.89[AMR][1000 genomes]
rs73043406	1.00[AMR][1000 genomes]
rs73043407	1.00[AMR][1000 genomes]
rs73043413	1.00[AMR][1000 genomes]
rs73045191	0.89[AMR][1000 genomes]
rs73045195	0.89[AMR][1000 genomes]
rs73045198	0.89[AMR][1000 genomes]
rs73059758	1.00[AMR][1000 genomes]
rs73059766	1.00[AMR][1000 genomes]
rs7355835	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883508	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883509	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73886620	1.00[AMR][1000 genomes]
rs7611533	0.89[AMR][1000 genomes]
rs7625719	1.00[AMR][1000 genomes]
rs9814990	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9815687	0.81[AFR][1000 genomes]
rs9829054	0.89[AMR][1000 genomes]
rs9834493	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861354	0.89[AMR][1000 genomes]
rs9864857	0.89[AMR][1000 genomes]
rs9872939	0.89[AMR][1000 genomes]
rs9884070	0.89[AMR][1000 genomes]
rs9968068	1.00[AMR][1000 genomes]
rs9968069	1.00[AMR][1000 genomes]
rs9968075	1.00[AMR][1000 genomes]
rs9968076	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179064000-179066400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:179064000-179066400	Active TSS	Fetal Muscle Trunk	muscle
3	chr3:179064000-179066600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:179064000-179066600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:179064000-179066600	Active TSS	Stomach Smooth Muscle	stomach
6	chr3:179064000-179066800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:179064000-179067000	Active TSS	GM12878-XiMat	blood
8	chr3:179064200-179066400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:179064200-179066400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:179064200-179066400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:179064200-179066400	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:179064200-179066400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:179064200-179066400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:179064200-179066400	Active TSS	Pancreas	Pancrea
15	chr3:179064200-179066600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr3:179064200-179066600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:179064200-179066600	Active TSS	Right Ventricle	heart
18	chr3:179064200-179066800	Active TSS	Colonic Mucosa	Colon
19	chr3:179064400-179066400	Active TSS	Esophagus	oesophagus
20	chr3:179064400-179066400	Active TSS	Fetal Intestine Small	intestine
21	chr3:179064400-179066400	Active TSS	Fetal Thymus	thymus
22	chr3:179064400-179066400	Active TSS	Left Ventricle	heart
23	chr3:179064400-179066400	Active TSS	Ovary	ovary
24	chr3:179064400-179066400	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr3:179064400-179066400	Active TSS	A549	lung
26	chr3:179064400-179066600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:179064400-179066600	Active TSS	Muscle Satellite Cultured Cells	--
28	chr3:179064400-179066600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:179064400-179066600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:179064400-179066600	Active TSS	Psoas Muscle	Psoas
31	chr3:179064400-179066600	Active TSS	NHDF-Ad	bronchial
32	chr3:179064400-179066800	Active TSS	NHLF	lung
33	chr3:179064600-179066400	Active TSS	Gastric	stomach
34	chr3:179064600-179066400	Active TSS	Lung	lung
35	chr3:179064800-179066400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:179065000-179066400	Active TSS	Primary B cells from peripheral blood	blood
37	chr3:179065200-179066400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:179065200-179066400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:179065200-179066400	Active TSS	K562	blood
40	chr3:179065200-179066600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr3:179065400-179066400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:179065800-179066400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr3:179065800-179066600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr3:179065800-179066600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr3:179065800-179066800	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr3:179065800-179066800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr3:179065800-179066800	Flanking Active TSS	Fetal Brain Female	brain
48	chr3:179065800-179066800	Active TSS	Right Atrium	heart
49	chr3:179066000-179066400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr3:179066000-179066400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links