Variant report

Variant	rs6882243
Chromosome Location	chr5:145558329-145558330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:145549719..145552981-chr5:145557063..145560291,4	MCF-7	breast:
2	chr5:145556363..145559212-chr5:145560408..145562154,3	K562	blood:
3	chr5:145558307..145563846-chr5:145580315..145584343,10	K562	blood:
4	chr5:145555213..145560576-chr5:145560598..145562206,4	K562	blood:
5	chr5:145557742..145559707-chr5:145585614..145588262,3	K562	blood:
6	chr5:145551306..145553774-chr5:145557195..145559625,2	K562	blood:
7	chr5:145558240..145560527-chr5:145600863..145603054,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000091009	Chromatin interaction
ENSG00000133706	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10515568	0.86[EUR][1000 genomes]
rs11540216	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11952903	0.86[EUR][1000 genomes]
rs11959720	0.86[EUR][1000 genomes]
rs17104247	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17104250	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17104260	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17104264	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17104266	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17104268	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17104276	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17104293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17104318	0.90[EUR][1000 genomes]
rs17104321	0.90[EUR][1000 genomes]
rs17104322	0.90[EUR][1000 genomes]
rs17104324	0.90[EUR][1000 genomes]
rs17104331	0.90[EUR][1000 genomes]
rs17104347	0.86[EUR][1000 genomes]
rs17104362	0.86[EUR][1000 genomes]
rs17104371	0.86[EUR][1000 genomes]
rs17104395	0.83[EUR][1000 genomes]
rs2163754	0.90[EUR][1000 genomes]
rs2895652	0.90[EUR][1000 genomes]
rs4631229	0.86[EUR][1000 genomes]
rs56864252	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57466173	0.86[EUR][1000 genomes]
rs57722184	0.93[EUR][1000 genomes]
rs58569901	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58922378	0.86[EUR][1000 genomes]
rs60892265	0.88[EUR][1000 genomes]
rs61455974	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66507348	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66891285	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67350755	0.90[EUR][1000 genomes]
rs67721586	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67859456	0.90[EUR][1000 genomes]
rs67897591	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs68040240	0.85[EUR][1000 genomes]
rs6870249	0.86[EUR][1000 genomes]
rs6871866	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72806113	0.86[EUR][1000 genomes]
rs72806116	0.86[EUR][1000 genomes]
rs72806136	0.86[EUR][1000 genomes]
rs72806144	0.86[EUR][1000 genomes]
rs72806155	0.86[EUR][1000 genomes]
rs72806173	0.85[EUR][1000 genomes]
rs72806176	0.83[EUR][1000 genomes]
rs72820451	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72820464	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72822208	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72822249	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72822252	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72822263	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72822274	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72822293	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72822296	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72824110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72824123	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72824124	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73315720	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73317887	0.93[EUR][1000 genomes]
rs73317890	0.93[EUR][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	nsv883006	chr5:145450586-145672431	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428128	chr5:145503978-145682880	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv883007	chr5:145506100-145672431	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv883008	chr5:145509728-145642925	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3348501	chr5:145543808-145572250	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145481200-145560200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:145491000-145560200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:145491200-145560200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:145491200-145560200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:145491200-145560800	Weak transcription	Stomach Mucosa	stomach
6	chr5:145491400-145560000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:145491400-145560400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:145491600-145559800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr5:145492200-145560200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:145495800-145559200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:145532200-145559600	Weak transcription	Small Intestine	intestine
12	chr5:145532200-145561000	Weak transcription	Esophagus	oesophagus
13	chr5:145535200-145559600	Strong transcription	Fetal Muscle Leg	muscle
14	chr5:145535600-145559600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:145537800-145560800	Weak transcription	Fetal Heart	heart
16	chr5:145541000-145560400	Weak transcription	Right Atrium	heart
17	chr5:145542600-145559600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:145542600-145560200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:145542600-145560400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:145542600-145560600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:145542800-145559600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:145542800-145561200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:145543000-145560200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:145543600-145560400	Weak transcription	Brain Angular Gyrus	brain
25	chr5:145544000-145560400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:145544000-145560400	Weak transcription	Psoas Muscle	Psoas
27	chr5:145544600-145559400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:145546200-145560200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:145546200-145560400	Weak transcription	Pancreas	Pancrea
30	chr5:145546400-145558800	Weak transcription	Brain Germinal Matrix	brain
31	chr5:145546800-145559000	Weak transcription	Fetal Brain Male	brain
32	chr5:145547000-145561000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr5:145547800-145558600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:145548000-145559600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:145548000-145561000	Weak transcription	NHLF	lung
36	chr5:145550000-145561000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr5:145550400-145561000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:145550600-145559200	Weak transcription	Gastric	stomach
39	chr5:145550600-145559600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:145550600-145560400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr5:145550600-145561000	Weak transcription	Colonic Mucosa	Colon
42	chr5:145550600-145561600	Weak transcription	Aorta	Aorta
43	chr5:145550600-145561600	Weak transcription	Colon Smooth Muscle	Colon
44	chr5:145550800-145559600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:145550800-145560400	Weak transcription	Right Ventricle	heart
46	chr5:145550800-145560400	Weak transcription	Spleen	Spleen
47	chr5:145550800-145560600	Weak transcription	Ovary	ovary
48	chr5:145550800-145561000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:145550800-145561000	Weak transcription	Fetal Kidney	kidney
50	chr5:145550800-145561000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links