Variant report

Variant	rs73729776
Chromosome Location	chr6:25171673-25171674
allele	C/T
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	GATA3	chr6:25171417-25172001	MCF-7	breast:	n/a	chr6:25171486-25171503
2	HDAC2	chr6:25171474-25171873	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr6:25171354-25171983	MCF-7	breast:	n/a	n/a
4	GATA3	chr6:25171477-25171860	T-47D	breast:	n/a	chr6:25171486-25171503
5	FOXA1	chr6:25171529-25171787	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25164181..25167866-chr6:25169101..25173283,5	MCF-7	breast:
2	chr20:46557528..46559114-chr6:25169864..25172495,2	MCF-7	breast:

Variant related genes	Relation type
CMAHP	TF binding region
ENSG00000168405	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16890188	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1880274	1.00[EUR][1000 genomes]
rs2394370	1.00[EUR][1000 genomes]
rs56145792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6456649	1.00[EUR][1000 genomes]
rs6456650	1.00[EUR][1000 genomes]
rs6941305	1.00[EUR][1000 genomes]
rs73729778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7753443	1.00[EUR][1000 genomes]
rs9461105	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461110	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9467436	1.00[EUR][1000 genomes]
rs9467437	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv462663	chr6:25156197-25234884	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv601167	chr6:25156197-25234884	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25164800-25173800	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:25165600-25177000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:25166000-25171800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr6:25166400-25174000	Weak transcription	Fetal Lung	lung
5	chr6:25167000-25173200	Weak transcription	Fetal Intestine Large	intestine
6	chr6:25167000-25173200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:25167000-25174400	Weak transcription	Aorta	Aorta
8	chr6:25167000-25177400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:25167600-25175400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:25167800-25172000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:25168800-25177000	Enhancers	Placenta	Placenta
12	chr6:25169000-25173200	Weak transcription	Fetal Intestine Small	intestine
13	chr6:25169000-25177000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr6:25169200-25171800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:25169200-25172200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:25169200-25173400	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr6:25169200-25177400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:25169600-25171800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:25169800-25171800	Enhancers	Liver	Liver
20	chr6:25169800-25172000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:25169800-25173400	Enhancers	HSMMtube	muscle
22	chr6:25170000-25177400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:25170200-25171800	Enhancers	Stomach Mucosa	stomach
24	chr6:25170200-25172600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:25170200-25173200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:25170200-25173600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:25170200-25174000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:25170400-25172000	Enhancers	Esophagus	oesophagus
29	chr6:25170400-25177000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:25170600-25171800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:25170600-25172600	Weak transcription	HSMM	muscle
32	chr6:25170600-25172600	Weak transcription	NH-A	brain
33	chr6:25170600-25172600	Weak transcription	NHLF	lung
34	chr6:25170600-25173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:25170800-25172800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:25170800-25173000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:25170800-25173200	Weak transcription	Ovary	ovary
38	chr6:25170800-25174400	Weak transcription	Pancreas	Pancrea
39	chr6:25170800-25174600	Weak transcription	Lung	lung
40	chr6:25170800-25175000	Weak transcription	Thymus	Thymus
41	chr6:25171000-25172000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:25171000-25173200	Weak transcription	Fetal Thymus	thymus
43	chr6:25171200-25173000	Weak transcription	Osteobl	bone
44	chr6:25171200-25173400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:25171200-25174000	Enhancers	NHDF-Ad	bronchial
46	chr6:25171400-25172000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr6:25171400-25172000	Enhancers	Gastric	stomach
48	chr6:25171400-25173000	Enhancers	NHEK	skin
49	chr6:25171400-25177000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:25171400-25177200	Enhancers	HMEC	breast

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