Variant report

Variant	rs62130187
Chromosome Location	chr2:10544007-10544008
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10539200..10541759-chr2:10543040..10545009,3	K562	blood:
2	chr2:10543371..10546081-chr2:10546266..10548397,3	K562	blood:
3	chr2:10543950..10547023-chr2:10547884..10550475,4	MCF-7	breast:
4	chr2:10524400..10527194-chr2:10542947..10545741,3	MCF-7	breast:
5	chr2:10537407..10539660-chr2:10542991..10544767,2	MCF-7	breast:
6	chr2:10538831..10544260-chr2:10544573..10548851,6	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11694643	0.93[ASN][1000 genomes]
rs13383055	0.88[ASN][1000 genomes]
rs13383253	0.88[ASN][1000 genomes]
rs17434886	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270303	0.93[ASN][1000 genomes]
rs3755261	0.93[ASN][1000 genomes]
rs3755262	0.93[ASN][1000 genomes]
rs3771123	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771126	0.95[ASN][1000 genomes]
rs3771135	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3771144	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771145	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771146	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821200	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55961729	0.88[ASN][1000 genomes]
rs56156675	0.88[ASN][1000 genomes]
rs56382508	0.88[ASN][1000 genomes]
rs62128251	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62128252	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62128254	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62130179	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62130183	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62130191	0.88[ASN][1000 genomes]
rs7579181	0.98[ASN][1000 genomes]
rs7599203	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7603265	0.98[ASN][1000 genomes]
rs7603352	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10530600-10544400	Weak transcription	Brain Angular Gyrus	brain
2	chr2:10531000-10544600	Weak transcription	NHLF	lung
3	chr2:10531200-10544200	Weak transcription	Brain Substantia Nigra	brain
4	chr2:10533000-10551800	Weak transcription	Ovary	ovary
5	chr2:10533400-10549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:10533600-10544200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:10533600-10544200	Weak transcription	Fetal Brain Female	brain
8	chr2:10534000-10545400	Weak transcription	Fetal Lung	lung
9	chr2:10538200-10544400	Weak transcription	Psoas Muscle	Psoas
10	chr2:10539400-10544800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:10539600-10544400	Weak transcription	Fetal Kidney	kidney
12	chr2:10540200-10544800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:10541000-10544200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:10541000-10544200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:10541000-10544400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:10541000-10547400	Weak transcription	K562	blood
17	chr2:10541200-10544200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:10541200-10544200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:10541200-10550800	Enhancers	Fetal Muscle Leg	muscle
20	chr2:10541400-10544400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:10541400-10545200	Weak transcription	Pancreas	Pancrea
22	chr2:10541400-10545200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:10541600-10544400	Weak transcription	Fetal Stomach	stomach
24	chr2:10541600-10545200	Enhancers	Osteobl	bone
25	chr2:10541800-10546400	Enhancers	Adipose Nuclei	Adipose
26	chr2:10541800-10546400	Weak transcription	Fetal Thymus	thymus
27	chr2:10541800-10547200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:10542000-10544200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:10542000-10544200	Weak transcription	Placenta	Placenta
30	chr2:10542000-10544200	Weak transcription	Thymus	Thymus
31	chr2:10542000-10544400	Weak transcription	Esophagus	oesophagus
32	chr2:10542000-10544600	Weak transcription	Right Atrium	heart
33	chr2:10542000-10546400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:10542000-10546600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:10542000-10547000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:10542000-10549400	Enhancers	HUVEC	blood vessel
37	chr2:10542200-10544200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:10542200-10544200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:10542200-10547600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:10542400-10546400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:10542400-10549400	Enhancers	NHDF-Ad	bronchial
42	chr2:10542600-10544200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:10542600-10544400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:10542600-10544400	Weak transcription	Gastric	stomach
45	chr2:10542600-10544400	Weak transcription	Right Ventricle	heart
46	chr2:10542600-10545400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:10542600-10545400	Weak transcription	Spleen	Spleen
48	chr2:10542600-10545600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:10542600-10546000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:10542600-10546400	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links