Variant report

Variant	rs2548349
Chromosome Location	chr5:42988302-42988303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:42988028..42998045-chr5:43036469..43045844,20	K562	blood:
2	chr5:42913658..42915671-chr5:42988106..42990787,2	K562	blood:
3	chr5:42986506..42989376-chr5:43041459..43043434,3	K562	blood:
4	chr5:42911041..42912693-chr5:42987765..42989682,2	K562	blood:
5	chr5:42909564..42912541-chr5:42988182..42990519,2	K562	blood:

Variant related genes	Relation type
ENSG00000215068	Chromatin interaction
ENSG00000177721	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10064003	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10522	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10941604	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10941605	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11747435	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11748821	0.82[EUR][1000 genomes]
rs11958008	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12697439	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13169690	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13170208	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13178479	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13179934	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1542369	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs160709	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs186323	0.86[ASN][1000 genomes]
rs186324	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1902101	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2100473	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124069	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs222060	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2247280	0.84[AMR][1000 genomes]
rs2253450	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2329994	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2329995	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2548334	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2548339	0.86[ASN][1000 genomes]
rs2548341	0.83[ASN][1000 genomes]
rs2548343	0.84[ASN][1000 genomes]
rs2548345	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548346	0.85[ASN][1000 genomes]
rs2548350	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2548353	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548356	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548373	0.85[AMR][1000 genomes]
rs2603620	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2603634	0.85[AMR][1000 genomes]
rs2603644	0.82[ASN][1000 genomes]
rs2603656	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2882295	0.83[ASN][1000 genomes]
rs2924817	0.82[AMR][1000 genomes]
rs309909	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309914	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs309921	0.86[AMR][1000 genomes]
rs309922	0.83[ASN][1000 genomes]
rs309923	0.86[ASN][1000 genomes]
rs309924	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs309925	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs309926	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs309927	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs309948	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316395	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs316414	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs316416	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs316419	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs316422	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3909456	0.81[ASN][1000 genomes]
rs4033115	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4092293	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4092294	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4296812	0.87[AMR][1000 genomes]
rs613825	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs643307	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6451660	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6451661	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6451662	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6875214	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs724430	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs768441	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7715065	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9292862	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
9	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
12	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
13	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
14	nsv881436	chr5:42967215-43008917	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
15	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
16	nsv881640	chr5:42978644-43028221	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
17	nsv880415	chr5:42978644-43030798	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42970800-42988400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:42982800-42989400	Weak transcription	Adipose Nuclei	Adipose
3	chr5:42982800-42990800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:42983000-42990000	Weak transcription	Fetal Thymus	thymus
5	chr5:42984400-42988600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:42984400-42989400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr5:42985400-42991400	Weak transcription	Placenta	Placenta
8	chr5:42985800-42988800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:42986000-42989000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:42986200-42988400	Weak transcription	Primary B cells from cord blood	blood
11	chr5:42986200-42988400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr5:42986200-42988600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr5:42986200-42988800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr5:42986200-42989200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:42986200-42989400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:42986200-42990000	Weak transcription	Spleen	Spleen
17	chr5:42986200-42990200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:42986400-42989000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:42986400-42989000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:42986400-42989400	Weak transcription	NH-A	brain
21	chr5:42986600-42989400	Weak transcription	Hela-S3	cervix
22	chr5:42986600-42989400	Weak transcription	NHDF-Ad	bronchial
23	chr5:42986600-42989400	Weak transcription	Osteobl	bone
24	chr5:42986800-42988600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:42986800-42991200	Weak transcription	NHLF	lung
26	chr5:42987000-42989400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:42987000-42990000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr5:42987200-42990200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:42987200-42992400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:42987400-42989400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:42987600-42988400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:42987600-42988400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:42987600-42989000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:42988000-42989600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:42988200-42988400	Active TSS	HUVEC	blood vessel
36	chr5:42988200-42988600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr5:42988200-42988600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr5:42988200-42988800	Enhancers	Primary T cells from cord blood	blood
39	chr5:42988200-42989600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr5:42988200-42989800	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links