Variant report

Variant	rs56257817
Chromosome Location	chr10:52168884-52168885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52164829..52166437-chr10:52168704..52170422,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs56040538	0.80[AFR][1000 genomes]
rs57185346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57222480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58417005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59310089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59583053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74131292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74131295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132715	0.83[AFR][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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' 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	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52142600-52170200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:52147000-52176600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:52156200-52170200	Weak transcription	Pancreas	Pancrea
4	chr10:52157000-52170800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr10:52157200-52170000	Weak transcription	Gastric	stomach
6	chr10:52157200-52177600	Weak transcription	Spleen	Spleen
7	chr10:52157400-52170000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr10:52157800-52169200	Weak transcription	HSMM	muscle
9	chr10:52157800-52172000	Weak transcription	Fetal Lung	lung
10	chr10:52157800-52173200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr10:52157800-52175400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr10:52157800-52176800	Weak transcription	Lung	lung
13	chr10:52158800-52169400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr10:52158800-52172200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:52160800-52176800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:52163200-52170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:52163400-52170000	Weak transcription	NHLF	lung
18	chr10:52163600-52176800	Weak transcription	Thymus	Thymus
19	chr10:52164400-52170000	Weak transcription	Brain Substantia Nigra	brain
20	chr10:52164400-52170000	Enhancers	Hela-S3	cervix
21	chr10:52164400-52170200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr10:52164400-52172400	Weak transcription	Ovary	ovary
23	chr10:52164400-52173800	Weak transcription	Psoas Muscle	Psoas
24	chr10:52164400-52174000	Weak transcription	Brain Angular Gyrus	brain
25	chr10:52164400-52177600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr10:52164600-52169000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:52164600-52171000	Weak transcription	Brain Hippocampus Middle	brain
28	chr10:52164600-52176600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr10:52165200-52171600	Weak transcription	Brain Anterior Caudate	brain
30	chr10:52165400-52171800	Weak transcription	Liver	Liver
31	chr10:52166200-52169800	Weak transcription	Esophagus	oesophagus
32	chr10:52166200-52170000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr10:52166400-52170000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:52166400-52170000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr10:52166400-52170200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr10:52166400-52170200	Genic enhancers	K562	blood
37	chr10:52166600-52170400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr10:52166600-52175800	Weak transcription	Primary T cells from cord blood	blood
39	chr10:52166600-52177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr10:52166800-52171400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr10:52166800-52177200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr10:52166800-52177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr10:52167000-52170000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr10:52167000-52176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr10:52167000-52176800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr10:52167000-52177200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr10:52167000-52177400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr10:52167600-52169000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr10:52167600-52169200	Weak transcription	A549	lung
50	chr10:52167600-52170000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links