Variant report

Variant	rs159972
Chromosome Location	chr5:152732406-152732407
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	chr5:152723819..152726556-chr5:152729942..152732962,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12187528	0.81[AFR][1000 genomes]
rs1381540	0.88[EUR][1000 genomes]
rs1462113	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1462114	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs149095	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs150618	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159759	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159978	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs160066	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs160163	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs160172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2546328	0.82[EUR][1000 genomes]
rs2560231	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2926287	0.88[EUR][1000 genomes]
rs2926288	0.88[EUR][1000 genomes]
rs2927172	0.88[EUR][1000 genomes]
rs2964817	0.88[EUR][1000 genomes]
rs2973148	0.89[EUR][1000 genomes]
rs2973149	0.88[EUR][1000 genomes]
rs300326	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs300328	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs300331	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs300332	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs300334	0.99[ASN][1000 genomes]
rs300335	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs302738	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs304862	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304863	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs308270	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs982494	0.88[EUR][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	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1019051	chr5:152550863-153057896	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv868912	chr5:152582002-153095306	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv883052	chr5:152696107-152749009	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv883053	chr5:152696107-152806220	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152729800-152732800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr5:152730200-152734200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:152730800-152733200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:152732000-152732800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
5	chr5:152732000-152732800	Active TSS	Aorta	Aorta
6	chr5:152732000-152732800	Flanking Active TSS	HMEC	breast
7	chr5:152732000-152732800	Flanking Active TSS	NHEK	skin
8	chr5:152732000-152733000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:152732000-152733400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:152732200-152732600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:152732200-152732600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:152732200-152732600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:152732200-152732600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:152732200-152732600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:152732200-152732600	Active TSS	Brain Hippocampus Middle	brain
16	chr5:152732200-152732600	Active TSS	Esophagus	oesophagus
17	chr5:152732200-152732600	Enhancers	Fetal Brain Male	brain
18	chr5:152732200-152732600	Bivalent Enhancer	Left Ventricle	heart
19	chr5:152732200-152732600	Active TSS	Right Atrium	heart
20	chr5:152732200-152732600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
21	chr5:152732200-152732800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:152732200-152732800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:152732200-152732800	Active TSS	Primary T cells fromperipheralblood	blood
24	chr5:152732200-152732800	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr5:152732200-152732800	Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr5:152732200-152732800	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr5:152732200-152732800	Active TSS	Right Ventricle	heart
28	chr5:152732200-152732800	Active TSS	Osteobl	bone
29	chr5:152732200-152733000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:152732200-152733000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:152732200-152733000	Enhancers	Fetal Heart	heart
32	chr5:152732200-152733200	Flanking Active TSS	GM12878-XiMat	blood
33	chr5:152732400-152732600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr5:152732400-152732600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr5:152732400-152732600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr5:152732400-152732600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
37	chr5:152732400-152732600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:152732400-152732600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr5:152732400-152732600	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr5:152732400-152732600	Enhancers	Gastric	stomach
41	chr5:152732400-152732800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr5:152732400-152732800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:152732400-152732800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:152732400-152732800	Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr5:152732400-152732800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:152732400-152732800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:152732400-152732800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr5:152732400-152732800	Enhancers	NH-A	brain
49	chr5:152732400-152733000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr5:152732400-152733000	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links