Variant report

Variant	rs1633012
Chromosome Location	chr6:29758726-29758727
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	JUND	chr6:29758234-29759061	HCT-116	colon:	n/a	chr6:29758603-29758611 chr6:29758601-29758613 chr6:29758604-29758615
2	SP1	chr6:29758248-29759060	HCT-116	colon:	n/a	n/a
3	FOSL1	chr6:29758318-29758980	HCT-116	colon:	n/a	chr6:29758603-29758611 chr6:29758601-29758613 chr6:29758604-29758615
4	POLR2A	chr6:29758493-29758820	Hela-S3	cervix:	n/a	n/a
5	FOSL2	chr6:29758452-29758779	HepG2	liver:	n/a	chr6:29758603-29758611 chr6:29758601-29758613 chr6:29758604-29758615
6	EP300	chr6:29758315-29758906	ECC-1	luminal epithelium:	n/a	chr6:29758593-29758600
7	FOSL1	chr6:29758249-29759360	HCT-116	colon:	n/a	chr6:29758603-29758611 chr6:29758601-29758613 chr6:29758604-29758615
8	POLR2A	chr6:29758360-29758847	HCT-116	colon:	n/a	n/a
9	TEAD4	chr6:29758423-29758862	ECC-1	luminal epithelium:	n/a	chr6:29758571-29758580
10	FOS	chr6:29758430-29758782	MCF10A-Er-Src	breast:	n/a	chr6:29758603-29758611 chr6:29758601-29758613 chr6:29758604-29758615
11	FOS	chr6:29758430-29759272	MCF10A-Er-Src	breast:	n/a	chr6:29758603-29758611 chr6:29758601-29758613 chr6:29758604-29758615
12	MAX	chr6:29758239-29758907	HCT-116	colon:	n/a	n/a
13	TEAD4	chr6:29758388-29758848	HCT-116	colon:	n/a	chr6:29758571-29758580
14	SP1	chr6:29758289-29759050	HCT-116	colon:	n/a	n/a
15	FOS	chr6:29758431-29759264	MCF10A-Er-Src	breast:	n/a	chr6:29758603-29758611 chr6:29758601-29758613 chr6:29758604-29758615
16	TEAD4	chr6:29758353-29758841	ECC-1	luminal epithelium:	n/a	chr6:29758571-29758580
17	POLR2A	chr6:29758495-29758758	Hela-S3	cervix:	n/a	n/a
18	YY1	chr6:29758443-29758749	HCT-116	colon:	n/a	n/a
19	FOS	chr6:29758418-29758753	MCF10A-Er-Src	breast:	n/a	chr6:29758603-29758611 chr6:29758601-29758613 chr6:29758604-29758615
20	STAT3	chr6:29758474-29758773	MCF10A-Er-Src	breast:	n/a	n/a
21	TCF12	chr6:29758350-29758829	ECC-1	luminal epithelium:	n/a	n/a
22	JUND	chr6:29758286-29758923	HCT-116	colon:	n/a	chr6:29758603-29758611 chr6:29758601-29758613 chr6:29758604-29758615
23	TEAD4	chr6:29758297-29758873	HCT-116	colon:	n/a	chr6:29758571-29758580
24	POLR2A	chr6:29758421-29758789	HCT-116	colon:	n/a	n/a
25	STAT3	chr6:29758473-29758782	MCF10A-Er-Src	breast:	n/a	n/a
26	CEBPB	chr6:29758432-29758726	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29755459..29758755-chr6:29758827..29760410,3	MCF-7	breast:

Variant related genes	Relation type
HLA-V	TF binding region
ENSG00000181126	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1233330	0.87[EUR][1000 genomes]
rs1233334	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1610603	0.82[EUR][1000 genomes]
rs1610604	0.82[EUR][1000 genomes]
rs1610605	0.82[EUR][1000 genomes]
rs1610607	0.82[EUR][1000 genomes]
rs1610613	0.82[EUR][1000 genomes]
rs1610623	0.83[EUR][1000 genomes]
rs1610626	0.83[EUR][1000 genomes]
rs1610627	0.83[EUR][1000 genomes]
rs1610630	0.83[EUR][1000 genomes]
rs1610632	0.82[EUR][1000 genomes]
rs1610728	0.83[EUR][1000 genomes]
rs1610737	0.83[EUR][1000 genomes]
rs1610738	0.83[EUR][1000 genomes]
rs1610740	0.85[ASN][1000 genomes]
rs1611278	0.83[EUR][1000 genomes]
rs1611279	0.83[EUR][1000 genomes]
rs1611292	0.85[EUR][1000 genomes]
rs1611293	0.83[EUR][1000 genomes]
rs1611294	0.83[EUR][1000 genomes]
rs1611297	0.83[EUR][1000 genomes]
rs1625607	0.83[EUR][1000 genomes]
rs1625636	0.82[EUR][1000 genomes]
rs1626636	0.83[EUR][1000 genomes]
rs1632958	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1632971	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632972	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632984	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633017	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1633025	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1633026	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1633036	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1633038	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1633042	0.80[EUR][1000 genomes]
rs1633043	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1633045	0.83[EUR][1000 genomes]
rs1633046	0.83[EUR][1000 genomes]
rs1633048	0.83[EUR][1000 genomes]
rs1633049	0.83[EUR][1000 genomes]
rs1633050	0.83[EUR][1000 genomes]
rs1633051	0.83[EUR][1000 genomes]
rs1633052	0.83[EUR][1000 genomes]
rs1633055	0.83[EUR][1000 genomes]
rs1633056	0.83[EUR][1000 genomes]
rs1633057	0.83[EUR][1000 genomes]
rs1633058	0.83[EUR][1000 genomes]
rs1633060	0.83[EUR][1000 genomes]
rs1633061	0.83[EUR][1000 genomes]
rs1633062	0.83[EUR][1000 genomes]
rs1633064	0.83[EUR][1000 genomes]
rs1633069	0.82[EUR][1000 genomes]
rs1633076	0.83[EUR][1000 genomes]
rs1633091	0.81[EUR][1000 genomes]
rs1707	0.85[EUR][1000 genomes]
rs1736910	0.82[EUR][1000 genomes]
rs1736911	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1736914	0.82[EUR][1000 genomes]
rs1736916	0.82[EUR][1000 genomes]
rs1736952	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1736962	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736965	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736995	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737022	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1737039	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1737058	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1737060	0.81[EUR][1000 genomes]
rs1737065	0.83[EUR][1000 genomes]
rs1737066	0.83[EUR][1000 genomes]
rs1737067	0.82[EUR][1000 genomes]
rs1737068	0.83[EUR][1000 genomes]
rs1737070	0.83[EUR][1000 genomes]
rs1737071	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1737073	0.83[EUR][1000 genomes]
rs1737074	0.83[EUR][1000 genomes]
rs1737075	0.83[EUR][1000 genomes]
rs1737079	0.83[EUR][1000 genomes]
rs1737081	0.83[EUR][1000 genomes]
rs1737084	0.83[EUR][1000 genomes]
rs1737087	0.83[EUR][1000 genomes]
rs2248693	0.82[EUR][1000 genomes]
rs2735050	0.83[EUR][1000 genomes]
rs2743931	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3094166	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3094168	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3094656	0.82[EUR][1000 genomes]
rs3115629	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3117297	0.85[ASN][1000 genomes]
rs3117303	0.85[ASN][1000 genomes]
rs3128888	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3128902	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3128904	0.83[EUR][1000 genomes]
rs3128908	0.83[EUR][1000 genomes]
rs3128911	0.83[EUR][1000 genomes]
rs3128912	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3129184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130252	0.85[ASN][1000 genomes]
rs3131858	0.83[EUR][1000 genomes]
rs3131862	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3135050	0.85[ASN][1000 genomes]
rs394146	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs452850	0.89[AFR][1000 genomes]
rs56388903	0.87[EUR][1000 genomes]
rs6933762	0.83[EUR][1000 genomes]
rs733840	0.83[EUR][1000 genomes]
rs733841	0.83[EUR][1000 genomes]
rs909723	0.83[EUR][1000 genomes]
rs909724	0.80[EUR][1000 genomes]
rs909725	0.83[EUR][1000 genomes]
rs909726	0.83[EUR][1000 genomes]
rs909727	0.83[EUR][1000 genomes]
rs909732	0.82[EUR][1000 genomes]
rs909735	0.82[EUR][1000 genomes]
rs9258243	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs932338	0.81[EUR][1000 genomes]
rs932341	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	esv11180	chr6:29729381-29800066	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	esv3423001	chr6:29733216-29878601	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	esv3475027	chr6:29733297-29922699	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	esv3475028	chr6:29733297-29922699	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
15	esv3420260	chr6:29734457-29835593	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	esv3330285	chr6:29736281-29881328	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
17	nsv883536	chr6:29746023-29760819	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv883537	chr6:29746023-29767611	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv883538	chr6:29748206-29760819	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv883539	chr6:29748206-29780529	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	esv3396224	chr6:29754243-29888093	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
22	nsv965702	chr6:29758408-29798943	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29757400-29759000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:29757800-29758800	Enhancers	Hela-S3	cervix
3	chr6:29758000-29759000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:29758400-29759000	Flanking Active TSS	HMEC	breast
5	chr6:29758400-29759400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:29758400-29760000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:29758600-29758800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:29758600-29758800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:29758600-29758800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:29758600-29758800	Enhancers	Gastric	stomach
11	chr6:29758600-29759000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:29758600-29759200	Flanking Active TSS	NHEK	skin
13	chr6:29758600-29759400	Enhancers	Esophagus	oesophagus
14	chr6:29758600-29759400	Enhancers	Pancreas	Pancrea
15	chr6:29758600-29759600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:29758600-29759800	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr6:29758600-29760600	Active TSS	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links