Variant report

Variant	rs13309885
Chromosome Location	chr7:6117595-6117596
allele	A/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	CEBPB	chr7:6116748-6117602	A549	lung:	n/a	n/a
2	GTF3C2	chr7:6116526-6117610	Hela-S3	cervix:	n/a	n/a
3	CHD1	chr7:6116684-6117607	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6096078..6098948-chr7:6116857..6121575,6	K562	blood:
2	chr7:6115370..6118556-chr7:6119697..6122201,4	MCF-7	breast:
3	chr7:6090422..6101465-chr7:6116449..6124326,16	K562	blood:
4	chr7:6098532..6100576-chr7:6116384..6118671,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231704	TF binding region
ENSG00000086232	Chromatin interaction
ENSG00000252929	Chromatin interaction
ENSG00000231704	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11971500	1.00[AMR][1000 genomes]
rs11972027	1.00[AMR][1000 genomes]
rs11974287	1.00[AMR][1000 genomes]
rs11980833	1.00[AMR][1000 genomes]
rs17136039	1.00[AMR][1000 genomes]
rs34260367	1.00[AMR][1000 genomes]
rs60874263	1.00[AMR][1000 genomes]
rs6957141	1.00[AMR][1000 genomes]
rs6957720	1.00[AMR][1000 genomes]
rs6957737	1.00[AMR][1000 genomes]
rs6970518	1.00[AMR][1000 genomes]
rs7776722	1.00[AMR][1000 genomes]
rs7781006	1.00[AMR][1000 genomes]
rs7786901	1.00[AMR][1000 genomes]
rs7798762	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
2	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
3	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
5	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
7	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
8	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
9	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
10	nsv1034916	chr7:5934780-6158970	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
11	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
12	nsv1018388	chr7:6038713-6131169	Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
13	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
14	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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	64 gene(s)	inside rSNPs	diseases
15	esv3405881	chr7:6087760-6122016	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
16	nsv5628	chr7:6105462-6147148	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6111400-6119800	Weak transcription	K562	blood
2	chr7:6114600-6120400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:6115200-6118200	Weak transcription	Primary B cells from cord blood	blood
4	chr7:6115800-6117800	Enhancers	Placenta	Placenta
5	chr7:6116600-6117600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:6116600-6117600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:6116600-6117600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:6116600-6117600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:6116600-6117600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:6116600-6117600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr7:6116600-6117600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:6116600-6117600	Flanking Active TSS	Hela-S3	cervix
13	chr7:6116600-6117600	Flanking Active TSS	HepG2	liver
14	chr7:6116600-6117800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:6116600-6118000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr7:6116800-6117600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:6116800-6117600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:6117000-6117600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr7:6117000-6117600	Enhancers	HMEC	breast
20	chr7:6117000-6117600	Enhancers	NHEK	skin
21	chr7:6117000-6117600	Enhancers	Osteobl	bone
22	chr7:6117200-6117600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:6117200-6117600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr7:6117200-6117600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:6117200-6120000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:6117200-6120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:6117200-6120000	Weak transcription	Brain Substantia Nigra	brain
28	chr7:6117400-6117600	Enhancers	A549	lung
29	chr7:6117400-6117600	Enhancers	NH-A	brain
30	chr7:6117400-6120000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:6117400-6120000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:6117400-6120000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:6117400-6120000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:6117400-6120000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:6117400-6120000	Weak transcription	Adipose Nuclei	Adipose
36	chr7:6117400-6120000	Weak transcription	Esophagus	oesophagus
37	chr7:6117400-6120000	Weak transcription	NHDF-Ad	bronchial
38	chr7:6117400-6120200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr7:6117400-6120200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr7:6117400-6120200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr7:6117400-6120200	Weak transcription	NHLF	lung
42	chr7:6117400-6120400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:6117400-6120600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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