Variant report

Variant	rs56959268
Chromosome Location	chr10:5651305-5651306
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5648567..5652209-chr10:5653862..5656338,4	MCF-7	breast:
2	chr10:5637418..5639003-chr10:5650901..5653188,2	MCF-7	breast:
3	chr10:5486648..5491055-chr10:5645215..5653179,9	MCF-7	breast:
4	chr10:5641054..5644302-chr10:5649711..5652156,3	MCF-7	breast:
5	chr10:5634973..5639659-chr10:5649443..5654538,7	MCF-7	breast:
6	chr10:5648373..5651329-chr10:5728348..5730813,2	K562	blood:
7	chr10:5533616..5541618-chr10:5644676..5651501,11	MCF-7	breast:
8	chr10:5649482..5652224-chr10:5658930..5660591,2	MCF-7	breast:
9	chr10:5649787..5651799-chr10:5653744..5655689,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000178372	Chromatin interaction
ENSG00000173848	Chromatin interaction
ENSG00000228951	Chromatin interaction
ENSG00000242147	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11592918	0.86[ASN][1000 genomes]
rs11597142	0.93[AMR][1000 genomes]
rs11597151	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11597288	0.86[ASN][1000 genomes]
rs11599647	0.86[ASN][1000 genomes]
rs41289343	0.99[ASN][1000 genomes]
rs55876438	0.99[ASN][1000 genomes]
rs56187312	0.84[ASN][1000 genomes]
rs56243537	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58786423	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv894798	chr10:5503610-5670275	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv523491	chr10:5542109-5720067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	esv2757364	chr10:5557024-5720512	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS 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	33 gene(s)	inside rSNPs	diseases
7	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1036798	chr10:5637870-5652754	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1040932	chr10:5637870-5665774	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv466718	chr10:5639907-5657527	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv549890	chr10:5639907-5657527	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2753567	chr10:5641348-5652237	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv894806	chr10:5643511-5670275	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1054888	chr10:5645033-5694612	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv466719	chr10:5645895-5662915	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv549891	chr10:5645895-5662915	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv519582	chr10:5646103-5720067	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv894807	chr10:5647942-5691135	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv8599	chr10:5649129-5719928	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
20	nsv1050965	chr10:5649760-5717125	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 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	chr10:5639800-5651600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr10:5645000-5651800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr10:5648600-5652000	Weak transcription	Lung	lung
4	chr10:5649000-5652000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:5649000-5657400	Weak transcription	Left Ventricle	heart
6	chr10:5650000-5651600	Enhancers	Stomach Mucosa	stomach
7	chr10:5650000-5653000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr10:5650200-5662600	Enhancers	Fetal Muscle Leg	muscle
9	chr10:5650400-5651400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:5650400-5651400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:5650400-5651800	Enhancers	Esophagus	oesophagus
12	chr10:5650400-5651800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr10:5650400-5653000	Enhancers	NHDF-Ad	bronchial
14	chr10:5650400-5661800	Enhancers	Fetal Muscle Trunk	muscle
15	chr10:5650600-5651600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:5650600-5651600	Enhancers	NHEK	skin
17	chr10:5650600-5651800	Enhancers	Fetal Intestine Large	intestine
18	chr10:5650600-5651800	Enhancers	Small Intestine	intestine
19	chr10:5650600-5652000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr10:5650600-5652400	Enhancers	Aorta	Aorta
21	chr10:5650600-5653200	Enhancers	Liver	Liver
22	chr10:5650600-5653200	Enhancers	Fetal Intestine Small	intestine
23	chr10:5650800-5651600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:5650800-5651800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:5650800-5652000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:5650800-5655600	Weak transcription	Adipose Nuclei	Adipose
27	chr10:5651000-5651400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr10:5651000-5651400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:5651000-5651400	Enhancers	A549	lung
30	chr10:5651000-5651600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:5651000-5651600	Enhancers	Duodenum Mucosa	Duodenum
32	chr10:5651000-5652200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:5651000-5652200	Enhancers	Ovary	ovary
34	chr10:5651000-5652400	Flanking Active TSS	HMEC	breast
35	chr10:5651200-5651600	Enhancers	Hela-S3	cervix
36	chr10:5651200-5651800	Enhancers	Fetal Thymus	thymus
37	chr10:5651200-5652000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr10:5651200-5652000	Enhancers	HepG2	liver
39	chr10:5651200-5652200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr10:5651200-5653400	Enhancers	Colonic Mucosa	Colon
41	chr10:5651200-5653400	Enhancers	Psoas Muscle	Psoas
42	chr10:5651200-5653600	Enhancers	Pancreas	Pancrea
43	chr10:5651200-5656000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links