Variant report

Variant	rs7540642
Chromosome Location	chr1:155616948-155616949
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155615343..155618275-chr1:155618571..155621306,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10796951	0.89[AFR][1000 genomes]
rs10796952	0.90[AFR][1000 genomes]
rs12136836	0.86[AFR][1000 genomes]
rs2666828	0.91[AFR][1000 genomes]
rs2686264	0.89[AFR][1000 genomes]
rs348188	0.86[AFR][1000 genomes]
rs348189	0.87[AFR][1000 genomes]
rs4638121	0.88[AFR][1000 genomes]
rs485353	0.85[AFR][1000 genomes]
rs492669	0.84[AFR][1000 genomes]
rs4971057	0.91[AFR][1000 genomes]
rs4971058	0.90[AFR][1000 genomes]
rs607036	0.89[AFR][1000 genomes]
rs617232	0.91[AFR][1000 genomes]
rs6427281	0.83[AFR][1000 genomes]
rs6427282	0.86[AFR][1000 genomes]
rs670787	0.87[AFR][1000 genomes]
rs7522259	0.89[AFR][1000 genomes]
rs9426928	0.87[AFR][1000 genomes]
rs9427219	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
4	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv946419	chr1:155561148-155630744	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
11	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155605000-155618000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:155607400-155621200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:155613200-155617400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:155614000-155621000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:155614600-155617000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:155614800-155617000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:155614800-155617000	Enhancers	NHEK	skin
8	chr1:155614800-155617200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:155614800-155618000	Enhancers	NH-A	brain
10	chr1:155614800-155618800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:155615000-155617000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:155615000-155618000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:155615200-155621600	Weak transcription	Aorta	Aorta
14	chr1:155615400-155617000	Flanking Active TSS	HMEC	breast
15	chr1:155615400-155618000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:155615400-155618000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:155615400-155628600	Weak transcription	Right Ventricle	heart
18	chr1:155615600-155628400	Weak transcription	Left Ventricle	heart
19	chr1:155615600-155628400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:155615800-155618000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:155615800-155618000	Weak transcription	HepG2	liver
22	chr1:155615800-155618000	Weak transcription	HSMMtube	muscle
23	chr1:155615800-155618200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:155615800-155620400	Weak transcription	Lung	lung
25	chr1:155616000-155618000	Weak transcription	Right Atrium	heart
26	chr1:155616000-155628200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:155616200-155618000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:155616200-155618200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:155616200-155620800	Weak transcription	Fetal Brain Male	brain
30	chr1:155616400-155617000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:155616400-155617600	Weak transcription	Hela-S3	cervix
32	chr1:155616400-155618000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:155616400-155618000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:155616400-155618000	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:155616400-155618000	Weak transcription	Fetal Brain Female	brain
36	chr1:155616400-155618000	Weak transcription	Fetal Stomach	stomach
37	chr1:155616400-155618200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:155616400-155618400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:155616400-155628800	Weak transcription	Small Intestine	intestine
40	chr1:155616600-155617400	Weak transcription	Placenta	Placenta
41	chr1:155616600-155617800	Weak transcription	HSMM	muscle
42	chr1:155616600-155617800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr1:155616600-155618000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:155616600-155618000	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:155616600-155618000	Weak transcription	A549	lung
46	chr1:155616600-155618000	Weak transcription	NHDF-Ad	bronchial
47	chr1:155616600-155618000	Weak transcription	Osteobl	bone
48	chr1:155616600-155618200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:155616600-155618200	Weak transcription	Brain Angular Gyrus	brain
50	chr1:155616600-155618200	Weak transcription	Brain Cingulate Gyrus	brain

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