Variant report

Variant	rs1839224
Chromosome Location	chr5:107552510-107552511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10056658	0.90[EUR][1000 genomes]
rs10057274	0.92[EUR][1000 genomes]
rs10057905	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10070565	0.92[EUR][1000 genomes]
rs10477889	0.91[EUR][1000 genomes]
rs10477894	0.90[EUR][1000 genomes]
rs12521975	0.91[EUR][1000 genomes]
rs13174270	0.92[EUR][1000 genomes]
rs2044711	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2122157	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs286762	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs286765	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs286766	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs286768	0.83[EUR][1000 genomes]
rs28868900	0.89[EUR][1000 genomes]
rs2922409	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2922410	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2922411	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2922413	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2922414	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2922415	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922416	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922419	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2922434	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2966794	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2966805	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2966806	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2966807	0.91[EUR][1000 genomes]
rs2966808	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2966809	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2966810	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2966811	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2966812	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2966815	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2966817	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2966819	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34019963	0.90[EUR][1000 genomes]
rs34088844	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35053804	0.92[EUR][1000 genomes]
rs35624833	0.91[EUR][1000 genomes]
rs35959276	0.90[EUR][1000 genomes]
rs3756573	0.91[EUR][1000 genomes]
rs399438	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4276393	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4385196	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4957750	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66855775	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6860212	0.92[EUR][1000 genomes]
rs715638	0.94[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	nsv534281	chr5:107357579-107674981	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv830441	chr5:107450392-107614557	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv882684	chr5:107521677-107695558	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv830442	chr5:107539150-107697020	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107516200-107584800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:107517000-107571800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr5:107546200-107553200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:107546600-107590800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr5:107547000-107577200	Weak transcription	Fetal Intestine Large	intestine
6	chr5:107548800-107556000	Weak transcription	Left Ventricle	heart
7	chr5:107549200-107578000	Weak transcription	Pancreas	Pancrea
8	chr5:107549400-107552600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:107549400-107552600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:107549400-107557600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:107549400-107561200	Weak transcription	Fetal Intestine Small	intestine
12	chr5:107550000-107552600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:107550200-107561400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:107550600-107552600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:107550800-107553000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr5:107550800-107559400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:107551000-107553400	Weak transcription	Fetal Lung	lung
18	chr5:107551200-107559000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:107551200-107569000	Weak transcription	Primary T cells from cord blood	blood
20	chr5:107551400-107560600	Weak transcription	Liver	Liver
21	chr5:107551400-107561600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr5:107551800-107553400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:107551800-107556000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:107551800-107567200	Weak transcription	Primary B cells from cord blood	blood
25	chr5:107551800-107568800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:107551800-107569600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:107552000-107578800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:107552000-107585000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:107552400-107553000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:107552400-107553000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:107552400-107553000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr5:107552400-107553000	Enhancers	HSMM	muscle
33	chr5:107552400-107553000	Enhancers	Osteobl	bone
34	chr5:107552400-107553200	Enhancers	Fetal Heart	heart
35	chr5:107552400-107553600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:107552400-107553600	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links