Variant report

Variant	rs294498
Chromosome Location	chr5:58876950-58876951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10059809	0.82[AMR][1000 genomes]
rs10065078	0.82[AMR][1000 genomes]
rs10805516	0.89[ASN][1000 genomes]
rs1395336	0.95[MEX][hapmap]
rs1395337	0.82[AMR][1000 genomes]
rs159194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs159196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs159197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs177077	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs177078	0.83[ASN][1000 genomes]
rs186078	0.92[ASN][1000 genomes]
rs190936	0.89[ASN][1000 genomes]
rs294477	0.92[ASN][1000 genomes]
rs294478	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs294479	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs294481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs294482	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs294483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs294484	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs294485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs294486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs294492	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs294494	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs294495	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs294496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs294497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs294499	0.99[ASN][1000 genomes]
rs294500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs294501	1.00[ASN][1000 genomes]
rs294502	0.96[ASN][1000 genomes]
rs295943	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs295946	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs295948	0.93[ASN][1000 genomes]
rs295950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs295951	0.93[ASN][1000 genomes]
rs295952	0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs295953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs295954	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs295955	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs295956	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs295957	0.93[ASN][1000 genomes]
rs295958	0.92[ASN][1000 genomes]
rs295959	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs295960	0.92[ASN][1000 genomes]
rs295961	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs295962	0.89[ASN][1000 genomes]
rs295963	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs295964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs295965	0.89[ASN][1000 genomes]
rs295966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs295967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs295968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs295969	0.89[ASN][1000 genomes]
rs295970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs295971	0.89[ASN][1000 genomes]
rs295972	0.89[ASN][1000 genomes]
rs295973	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs295974	0.89[ASN][1000 genomes]
rs295975	0.89[ASN][1000 genomes]
rs295978	0.96[ASN][1000 genomes]
rs295979	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs296406	0.86[CEU][hapmap]
rs298014	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298016	0.89[ASN][1000 genomes]
rs298017	0.89[ASN][1000 genomes]
rs298025	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298027	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298028	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298029	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298030	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298032	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298033	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298034	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs298036	0.83[ASN][1000 genomes]
rs298038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs298039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs298040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs298041	0.83[ASN][1000 genomes]
rs298043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs298044	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs298045	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs298046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs298047	0.83[ASN][1000 genomes]
rs298048	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298051	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs298052	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs298053	0.89[ASN][1000 genomes]
rs37569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs37570	0.93[ASN][1000 genomes]
rs37571	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs37579	0.82[ASW][hapmap];0.95[MEX][hapmap]
rs40215	0.82[ASW][hapmap]
rs431381	0.86[EUR][1000 genomes]
rs6858964	0.82[ASW][hapmap];0.95[MEX][hapmap]

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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58859200-58883400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:58859400-58884000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:58863200-58878400	Weak transcription	Stomach Mucosa	stomach
4	chr5:58867400-58879800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:58870600-58878600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:58870600-58879600	Weak transcription	Small Intestine	intestine
7	chr5:58872800-58880400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:58873000-58879600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:58873000-58880000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:58874400-58879400	Enhancers	Fetal Intestine Large	intestine
11	chr5:58874600-58877800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:58874600-58879600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:58874800-58877800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:58874800-58877800	Weak transcription	Fetal Intestine Small	intestine
15	chr5:58874800-58877800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:58875000-58880000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:58875400-58878600	Enhancers	Fetal Brain Male	brain
18	chr5:58875600-58879600	Weak transcription	Fetal Muscle Leg	muscle
19	chr5:58875800-58877200	Weak transcription	Fetal Brain Female	brain
20	chr5:58875800-58878600	Weak transcription	Hela-S3	cervix
21	chr5:58875800-58880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:58876000-58878600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:58876000-58879000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:58876000-58879400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:58876000-58879600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:58876000-58879600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:58876200-58877000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:58876200-58878800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:58876200-58879000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:58876200-58879200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:58876200-58879400	Weak transcription	Brain Anterior Caudate	brain
32	chr5:58876200-58879400	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:58876400-58877000	Active TSS	Psoas Muscle	Psoas
34	chr5:58876400-58877200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr5:58876400-58878600	Weak transcription	Brain Substantia Nigra	brain
36	chr5:58876400-58879400	Weak transcription	Brain Angular Gyrus	brain
37	chr5:58876600-58878400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:58876600-58878600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:58876600-58879400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr5:58876600-58879400	Weak transcription	Fetal Kidney	kidney
41	chr5:58876800-58878800	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links