Variant report

Variant	rs33939197
Chromosome Location	chr5:42496058-42496059
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	chr5:42493810..42496602-chr5:42496863..42498426,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs13153060	0.83[AFR][1000 genomes]
rs13168764	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171720	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13184352	1.00[ASN][1000 genomes]
rs13187542	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17574527	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17575164	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28943878	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28943880	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34126503	0.83[AFR][1000 genomes]
rs34161441	0.83[AFR][1000 genomes]
rs34305870	0.83[AFR][1000 genomes]
rs34975809	1.00[ASN][1000 genomes]
rs35003055	1.00[ASN][1000 genomes]
rs35185573	1.00[ASN][1000 genomes]
rs35331831	0.83[AFR][1000 genomes]
rs35525634	1.00[ASN][1000 genomes]
rs35920615	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129472	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129645	1.00[ASN][1000 genomes]
rs56144821	1.00[ASN][1000 genomes]
rs67005744	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67277863	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67314897	0.83[AFR][1000 genomes]
rs67812331	1.00[ASN][1000 genomes]
rs67846180	0.83[AFR][1000 genomes]
rs67871277	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6863381	1.00[ASN][1000 genomes]
rs6885716	0.83[AFR][1000 genomes]
rs6891036	0.83[AFR][1000 genomes]
rs72753062	0.83[AFR][1000 genomes]
rs72753064	0.83[AFR][1000 genomes]
rs7703669	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7716495	0.84[AFR][1000 genomes]
rs7718962	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9763260	1.00[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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42490600-42499200	Weak transcription	Pancreas	Pancrea
2	chr5:42490800-42499200	Weak transcription	Left Ventricle	heart
3	chr5:42491800-42496400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:42492000-42499200	Weak transcription	Right Atrium	heart
5	chr5:42492200-42496200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:42492200-42496600	Weak transcription	Liver	Liver
7	chr5:42492200-42499200	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:42492200-42499200	Weak transcription	Ovary	ovary
9	chr5:42493000-42496200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:42493200-42499800	Weak transcription	Fetal Lung	lung
11	chr5:42494000-42498400	Enhancers	Fetal Heart	heart
12	chr5:42494200-42496600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:42494200-42496800	Enhancers	NHEK	skin
14	chr5:42494400-42496800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:42494600-42496400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:42494600-42499000	Weak transcription	Adipose Nuclei	Adipose
17	chr5:42494800-42497200	Enhancers	Colon Smooth Muscle	Colon
18	chr5:42495200-42497000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:42495200-42500000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:42495400-42497600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:42495800-42496200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:42495800-42496400	Enhancers	HSMMtube	muscle
23	chr5:42495800-42496600	Enhancers	Rectal Smooth Muscle	rectum
24	chr5:42495800-42496800	Enhancers	HMEC	breast
25	chr5:42495800-42497200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr5:42495800-42497600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:42495800-42499200	Weak transcription	Right Ventricle	heart
28	chr5:42496000-42496600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:42496000-42498400	Enhancers	Psoas Muscle	Psoas
30	chr5:42496000-42501200	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links