Variant report

Variant	rs4949039
Chromosome Location	chr10:43361759-43361760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43360364..43363685-chr10:43571830..43575400,3	MCF-7	breast:
2	chr10:43359656..43362276-chr10:43538559..43540315,2	MCF-7	breast:
3	chr10:43361133..43364035-chr10:43632950..43635001,2	MCF-7	breast:
4	chr10:43355311..43356829-chr10:43360308..43362900,2	MCF-7	breast:
5	chr10:43360509..43362298-chr10:43627787..43629550,2	MCF-7	breast:
6	chr10:43360554..43363791-chr10:43570974..43576100,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169826	Chromatin interaction
ENSG00000273008	Chromatin interaction
ENSG00000165731	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12220767	0.96[ASN][1000 genomes]
rs12762093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12768318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12769004	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12771057	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12774126	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12774683	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12775553	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4119177	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4948691	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949036	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4949038	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949043	0.91[ASN][1000 genomes]
rs7393563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9733285	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS 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	40 gene(s)	inside rSNPs	diseases
2	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv1047838	chr10:43234590-43379219	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv947892	chr10:43358233-43368929	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43361200-43361800	Bivalent Enhancer	Fetal Brain Male	brain
2	chr10:43361200-43362000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:43361200-43362000	Bivalent Enhancer	Placenta	Placenta
4	chr10:43361400-43361800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr10:43361400-43361800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
6	chr10:43361400-43361800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
7	chr10:43361400-43361800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:43361400-43361800	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr10:43361400-43362000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
10	chr10:43361400-43362200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:43361400-43362600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:43361400-43362600	Bivalent/Poised TSS	Fetal Brain Female	brain
13	chr10:43361600-43361800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr10:43361600-43361800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr10:43361600-43361800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:43361600-43361800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr10:43361600-43361800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:43361600-43361800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
19	chr10:43361600-43361800	Active TSS	Primary hematopoietic stem cells	blood
20	chr10:43361600-43361800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr10:43361600-43361800	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr10:43361600-43361800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr10:43361600-43361800	Bivalent Enhancer	Adipose Nuclei	Adipose
24	chr10:43361600-43361800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr10:43361600-43361800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:43361600-43361800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
27	chr10:43361600-43361800	Bivalent Enhancer	Colonic Mucosa	Colon
28	chr10:43361600-43361800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr10:43361600-43361800	Bivalent Enhancer	Fetal Stomach	stomach
30	chr10:43361600-43361800	Bivalent Enhancer	Ovary	ovary
31	chr10:43361600-43361800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr10:43361600-43362000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr10:43361600-43362000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr10:43361600-43362000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
35	chr10:43361600-43362000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
36	chr10:43361600-43362000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr10:43361600-43362000	Bivalent Enhancer	Fetal Intestine Small	intestine
38	chr10:43361600-43362000	Enhancers	Gastric	stomach
39	chr10:43361600-43362200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr10:43361600-43362200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr10:43361600-43362200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:43361600-43362200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
43	chr10:43361600-43362200	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr10:43361600-43362200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr10:43361600-43362200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr10:43361600-43362200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:43361600-43362200	Bivalent Enhancer	Liver	Liver
48	chr10:43361600-43362200	Active TSS	Brain Anterior Caudate	brain
49	chr10:43361600-43362200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
50	chr10:43361600-43362200	Enhancers	Placenta Amnion	Placenta Amnion

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