Variant report

Variant	rs55676360
Chromosome Location	chr2:10539239-10539240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10537541..10541103-chr2:10547321..10550436,3	MCF-7	breast:
2	chr2:10538831..10544260-chr2:10544573..10548851,6	K562	blood:
3	chr2:10539200..10541759-chr2:10543040..10545009,3	K562	blood:
4	chr2:10409644..10411196-chr2:10538400..10540753,2	MCF-7	breast:
5	chr2:10427792..10430069-chr2:10536723..10539558,2	MCF-7	breast:
6	chr2:10537407..10539660-chr2:10542991..10544767,2	MCF-7	breast:
7	chr2:10528701..10530809-chr2:10537442..10539772,2	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3771136	0.81[ASN][1000 genomes]
rs3771140	0.86[ASN][1000 genomes]
rs3771143	0.87[ASN][1000 genomes]
rs3771148	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4668682	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873641	chr2:10480415-10544640	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv873643	chr2:10535481-10583160	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv873644	chr2:10537347-10576424	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10523000-10541000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:10527200-10542400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:10530000-10540800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:10530400-10540800	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:10530600-10539800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:10530600-10544400	Weak transcription	Brain Angular Gyrus	brain
7	chr2:10531000-10539800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:10531000-10540600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:10531000-10542400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:10531000-10544600	Weak transcription	NHLF	lung
11	chr2:10531200-10539800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:10531200-10542400	Weak transcription	HSMMtube	muscle
13	chr2:10531200-10542400	Weak transcription	NH-A	brain
14	chr2:10531200-10544200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:10531400-10539800	Weak transcription	HSMM	muscle
16	chr2:10531400-10541600	Weak transcription	Osteobl	bone
17	chr2:10533000-10540200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:10533000-10551800	Weak transcription	Ovary	ovary
19	chr2:10533400-10549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:10533600-10539800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:10533600-10539800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:10533600-10544200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:10533600-10544200	Weak transcription	Fetal Brain Female	brain
24	chr2:10533800-10539400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:10533800-10539800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:10533800-10539800	Weak transcription	Colonic Mucosa	Colon
27	chr2:10533800-10539800	Weak transcription	Right Atrium	heart
28	chr2:10533800-10539800	Weak transcription	HepG2	liver
29	chr2:10534000-10539400	Weak transcription	NHEK	skin
30	chr2:10534000-10539800	Weak transcription	HMEC	breast
31	chr2:10534000-10540600	Weak transcription	Esophagus	oesophagus
32	chr2:10534000-10540800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:10534000-10541000	Strong transcription	Fetal Intestine Small	intestine
34	chr2:10534000-10545400	Weak transcription	Fetal Lung	lung
35	chr2:10536000-10539400	Enhancers	Stomach Mucosa	stomach
36	chr2:10536000-10541400	Genic enhancers	Spleen	Spleen
37	chr2:10536200-10539600	Strong transcription	Primary T cells from cord blood	blood
38	chr2:10536200-10541600	Strong transcription	Fetal Stomach	stomach
39	chr2:10536600-10540600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:10536800-10540000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:10536800-10540400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:10537000-10540600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:10537000-10540600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:10537000-10543000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:10537000-10543400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr2:10537400-10540200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:10537400-10541200	Enhancers	Adipose Nuclei	Adipose
48	chr2:10537400-10542600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:10537400-10542600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr2:10537400-10542800	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links