Variant report

Variant	rs2253450
Chromosome Location	chr5:42993927-42993928
allele	A/G
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:42879448..42882053-chr5:42991985..42994094,2	K562	blood:
2	chr5:42913329..42916103-chr5:42993492..42995662,2	K562	blood:
3	chr5:42990996..42996897-chr5:43036694..43045949,13	K562	blood:
4	chr5:42974190..42975842-chr5:42991638..42994075,2	MCF-7	breast:
5	chr5:42991772..42994897-chr5:42997978..43001031,3	MCF-7	breast:
6	chr5:42988028..42998045-chr5:43036469..43045844,20	K562	blood:
7	chr5:42989723..42997135-chr5:43060250..43070296,19	K562	blood:
8	chr5:42992038..42994724-chr5:43120190..43122287,2	K562	blood:
9	chr5:42990973..42999044-chr5:43062393..43068169,17	K562	blood:
10	chr5:42989588..43001279-chr5:43004636..43014428,32	K562	blood:
11	chr5:42989969..42995303-chr5:43120044..43124152,6	K562	blood:
12	chr5:41924886..41927114-chr5:42991951..42994899,2	K562	blood:
13	chr5:42942640..42945683-chr5:42991617..42995259,4	K562	blood:
14	chr5:42941021..42945683-chr5:42991872..42995259,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215068	Chromatin interaction
ENSG00000272144	Chromatin interaction
ENSG00000177721	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000151876	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10064003	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10522	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10941604	0.87[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941605	0.86[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747435	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11958008	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12697439	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13169690	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13170208	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13171133	0.84[ASN][1000 genomes]
rs13178479	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13179934	0.90[ASN][1000 genomes]
rs1542369	0.91[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs160709	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs186323	0.86[ASN][1000 genomes]
rs186324	0.82[ASN][1000 genomes]
rs1902101	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100473	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124069	0.90[ASN][1000 genomes]
rs222060	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2329994	0.87[ASN][1000 genomes]
rs2329995	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548334	0.82[ASN][1000 genomes]
rs2548339	0.86[ASN][1000 genomes]
rs2548341	0.83[ASN][1000 genomes]
rs2548343	0.84[ASN][1000 genomes]
rs2548345	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548346	0.85[ASN][1000 genomes]
rs2548349	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548350	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548353	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548356	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603620	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2603644	0.82[ASN][1000 genomes]
rs2603656	0.91[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882295	0.83[ASN][1000 genomes]
rs309909	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs309914	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs309922	0.83[ASN][1000 genomes]
rs309923	0.86[ASN][1000 genomes]
rs309924	0.87[ASN][1000 genomes]
rs309925	0.87[ASN][1000 genomes]
rs309926	0.87[ASN][1000 genomes]
rs309927	0.87[ASN][1000 genomes]
rs309948	0.82[ASN][1000 genomes]
rs316395	0.87[ASN][1000 genomes]
rs316396	0.81[ASN][1000 genomes]
rs316414	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316416	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316419	0.87[ASN][1000 genomes]
rs316422	0.87[ASN][1000 genomes]
rs3909456	0.81[ASN][1000 genomes]
rs4033115	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4092293	0.89[ASN][1000 genomes]
rs4092294	0.89[ASN][1000 genomes]
rs4296812	0.84[ASN][1000 genomes]
rs613825	0.87[ASN][1000 genomes]
rs643307	0.89[ASN][1000 genomes]
rs6451660	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6451661	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6451662	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6875214	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs724430	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs768441	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7715065	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292862	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2253450	FLJ32255	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42988400-42996200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:42990200-42996000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:42990800-42996000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
4	chr5:42991000-42995600	Active TSS	Right Ventricle	heart
5	chr5:42991200-42995400	Active TSS	NHLF	lung
6	chr5:42991200-42995800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:42991200-42995800	Active TSS	Thymus	Thymus
8	chr5:42991400-42994600	Bivalent/Poised TSS	Left Ventricle	heart
9	chr5:42991400-42995400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
10	chr5:42991400-42995400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
11	chr5:42991400-42995600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:42991400-42995800	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr5:42991400-42995800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
14	chr5:42991600-42994800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:42991600-42995200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr5:42991600-42995400	Active TSS	NHDF-Ad	bronchial
17	chr5:42991600-42995600	Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr5:42991600-42995600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr5:42991600-42995600	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr5:42991600-42995800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:42991600-42995800	Active TSS	HSMMtube	muscle
22	chr5:42991800-42995200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr5:42991800-42995200	Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr5:42991800-42995200	Bivalent/Poised TSS	Fetal Kidney	kidney
25	chr5:42991800-42995200	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr5:42991800-42995600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:42991800-42995600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:42991800-42996000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
29	chr5:42992000-42995200	ZNF genes & repeats	HMEC	breast
30	chr5:42992000-42995400	Active TSS	Primary B cells from peripheral blood	blood
31	chr5:42992000-42995400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:42992000-42995400	Active TSS	Dnd41	blood
33	chr5:42992000-42995400	Active TSS	GM12878-XiMat	blood
34	chr5:42992000-42995400	Active TSS	Osteobl	bone
35	chr5:42992000-42995600	Active TSS	Aorta	Aorta
36	chr5:42992000-42995600	ZNF genes & repeats	NHEK	skin
37	chr5:42992000-42995800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr5:42992000-42995800	Active TSS	HSMM	muscle
39	chr5:42992000-42996200	Active TSS	A549	lung
40	chr5:42992200-42994800	Active TSS	Adipose Nuclei	Adipose
41	chr5:42992200-42995400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:42992200-42995600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:42992200-42995600	Bivalent/Poised TSS	Small Intestine	intestine
44	chr5:42992400-42994200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr5:42992600-42994000	Active TSS	Primary hematopoietic stem cells	blood
46	chr5:42992600-42995400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr5:42992600-42995400	Active TSS	K562	blood
48	chr5:42992600-42995800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:42992600-42995800	Bivalent/Poised TSS	Colonic Mucosa	Colon
50	chr5:42992600-42995800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links