Variant report

Variant	rs3132601
Chromosome Location	chr6:30745777-30745778
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr6:30745711-30746249	A549	lung:	n/a	n/a
2	CEBPB	chr6:30745665-30745822	A549	lung:	n/a	n/a
3	CEBPB	chr6:30745656-30745870	HepG2	liver:	n/a	n/a
4	EP300	chr6:30745706-30746258	T-47D	breast:	n/a	n/a
5	POLR2A	chr6:30745754-30746167	PANC-1	pancreas:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30742016..30748001-chr6:30748066..30750476,5	MCF-7	breast:
2	chr6:30744501..30746062-chr6:30781081..30782628,2	K562	blood:
3	chr6:30694210..30695985-chr6:30745346..30747310,2	K562	blood:
4	chr6:30725912..30728357-chr6:30744418..30747133,2	K562	blood:

No data

Variant related genes	Relation type
HCG20	TF binding region
ENSG00000228022	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs3094114	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3094115	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3094116	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3094122	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3095339	0.84[EUR][1000 genomes]
rs3130671	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130672	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131036	0.83[EUR][1000 genomes]
rs4248148	0.92[ASN][1000 genomes]
rs6906722	0.88[ASN][1000 genomes]
rs6911571	0.88[ASN][1000 genomes]
rs6911628	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6912077	0.88[ASN][1000 genomes]
rs9262172	0.82[AMR][1000 genomes]
rs9262184	0.88[ASN][1000 genomes]
rs9262185	0.88[ASN][1000 genomes]
rs9468829	0.87[ASN][1000 genomes]
rs9468834	0.87[ASN][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	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
10	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv884104	chr6:30740680-30753146	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30734800-30747400	Weak transcription	Liver	Liver
2	chr6:30737600-30746000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:30737600-30746000	Weak transcription	Fetal Lung	lung
4	chr6:30737600-30746000	Weak transcription	Gastric	stomach
5	chr6:30737600-30746000	Weak transcription	Lung	lung
6	chr6:30737600-30746000	Weak transcription	Pancreas	Pancrea
7	chr6:30737600-30746000	Weak transcription	Right Atrium	heart
8	chr6:30737600-30746000	Weak transcription	Right Ventricle	heart
9	chr6:30737600-30746000	Weak transcription	Spleen	Spleen
10	chr6:30737600-30746200	Weak transcription	Psoas Muscle	Psoas
11	chr6:30737600-30746600	Weak transcription	Aorta	Aorta
12	chr6:30737600-30749200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:30738000-30746000	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:30738000-30746400	Weak transcription	Esophagus	oesophagus
15	chr6:30738400-30747000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:30738600-30745800	Weak transcription	NH-A	brain
17	chr6:30738600-30746000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:30738600-30746000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:30738600-30747000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:30738600-30749200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:30738800-30746200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:30738800-30746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:30739000-30746000	Weak transcription	K562	blood
24	chr6:30740600-30746000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:30741000-30746000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:30741000-30749600	Weak transcription	Thymus	Thymus
27	chr6:30742000-30749000	Enhancers	HepG2	liver
28	chr6:30742200-30746200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:30742400-30746200	Enhancers	Hela-S3	cervix
30	chr6:30742600-30747400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:30742800-30746200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:30743000-30746200	Weak transcription	HSMMtube	muscle
33	chr6:30743200-30745800	Weak transcription	NHDF-Ad	bronchial
34	chr6:30743200-30746000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:30743200-30746000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:30743200-30746000	Weak transcription	Placenta	Placenta
37	chr6:30743200-30746000	Weak transcription	Left Ventricle	heart
38	chr6:30743200-30746000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:30743200-30746000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:30743200-30746200	Weak transcription	HSMM	muscle
41	chr6:30743200-30747600	Weak transcription	HMEC	breast
42	chr6:30743400-30746000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:30743400-30746000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:30743400-30746000	Weak transcription	NHLF	lung
45	chr6:30743400-30746200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:30743400-30747000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:30743400-30747000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:30743600-30746800	Weak transcription	NHEK	skin
49	chr6:30744000-30758000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr6:30744200-30746000	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links