Variant report

Variant	rs6534148
Chromosome Location	chr4:120544218-120544219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10013852	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021469	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434030	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434031	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434032	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10518332	0.90[ASN][1000 genomes]
rs10518333	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331661	0.86[AMR][1000 genomes]
rs13119104	0.90[AFR][1000 genomes]
rs13125819	0.90[AFR][1000 genomes]
rs17007472	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051276	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051278	0.90[ASN][1000 genomes]
rs17357002	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359764	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17359910	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17360333	0.84[EUR][1000 genomes]
rs2256645	0.83[AFR][1000 genomes]
rs2389871	0.88[AFR][1000 genomes]
rs2389872	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389876	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389877	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389878	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389884	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622497	0.83[AFR][1000 genomes]
rs2928991	0.90[AFR][1000 genomes]
rs2953290	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2953294	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3109370	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4102980	0.85[ASN][1000 genomes]
rs4146266	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834786	0.85[AFR][1000 genomes]
rs4834787	0.86[AFR][1000 genomes]
rs58613543	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58735454	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534145	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854072	0.92[AFR][1000 genomes]
rs72922580	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72922588	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72922598	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7439678	0.90[AFR][1000 genomes]
rs7694813	0.85[AFR][1000 genomes]
rs8180145	0.90[ASN][1000 genomes]
rs8180147	0.90[ASN][1000 genomes]
rs9307480	0.96[AFR][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:120521000-120544800	Weak transcription	Fetal Intestine Large	intestine
3	chr4:120526200-120546800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:120528400-120547400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:120528600-120547400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:120528600-120547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:120528800-120545400	Weak transcription	Fetal Stomach	stomach
8	chr4:120529000-120546600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:120532400-120547600	Weak transcription	Lung	lung
10	chr4:120533600-120547400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:120534000-120547400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:120537000-120547400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:120539600-120545000	Weak transcription	Fetal Intestine Small	intestine
14	chr4:120540000-120544600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:120540600-120544800	Weak transcription	NHDF-Ad	bronchial
16	chr4:120541200-120544400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:120541400-120547600	Weak transcription	Left Ventricle	heart
18	chr4:120541800-120544400	Weak transcription	Aorta	Aorta
19	chr4:120542600-120545200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:120542600-120547800	Weak transcription	Small Intestine	intestine
21	chr4:120542800-120545000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:120542800-120546600	Weak transcription	Right Atrium	heart
23	chr4:120542800-120547600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:120543200-120547000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:120543200-120547600	Weak transcription	Pancreas	Pancrea
26	chr4:120544000-120544400	Enhancers	Osteobl	bone
27	chr4:120544000-120544800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:120544200-120544400	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr4:120544200-120544400	Active TSS	Stomach Smooth Muscle	stomach
30	chr4:120544200-120544600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr4:120544200-120544600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr4:120544200-120544800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:120544200-120544800	Enhancers	Duodenum Mucosa	Duodenum
34	chr4:120544200-120544800	Enhancers	NH-A	brain
35	chr4:120544200-120545200	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr4:120544200-120545200	Transcr. at gene 5' and 3'	NHLF	lung
37	chr4:120544200-120545400	Flanking Active TSS	Rectal Smooth Muscle	rectum
38	chr4:120544200-120545800	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links