Variant report

Variant	rs10514859
Chromosome Location	chr5:58879822-58879823
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58879018..58880553-chr5:58887523..58890077,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1035321	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491440	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491441	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491442	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950308	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11951110	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956402	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957151	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514190	1.00[ASN][1000 genomes]
rs12520633	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439074	0.88[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741863	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797996	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17798319	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41404047	0.83[CEU][hapmap];0.94[MEX][hapmap]
rs56007967	1.00[ASN][1000 genomes]
rs62355561	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355562	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355581	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355582	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355584	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357524	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357525	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357527	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357530	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62372240	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751212	1.00[ASN][1000 genomes]
rs72769726	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72769729	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs893190	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953302	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];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	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:55 , 50 per page) page: 1 2

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	chr5:58872800-58880400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:58873000-58880000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:58875000-58880000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:58875800-58880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:58878400-58882600	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr5:58878600-58880000	Enhancers	Liver	Liver
9	chr5:58878600-58880000	Active TSS	Brain Germinal Matrix	brain
10	chr5:58878600-58880200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr5:58878600-58880400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:58878600-58880400	Enhancers	Fetal Lung	lung
13	chr5:58878600-58881400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr5:58878800-58880200	Active TSS	A549	lung
15	chr5:58878800-58888200	Active TSS	Psoas Muscle	Psoas
16	chr5:58879000-58880400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:58879000-58882800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:58879000-58882800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:58879000-58884200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr5:58879200-58883800	Active TSS	Fetal Brain Female	brain
21	chr5:58879200-58884800	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr5:58879200-58885000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:58879400-58880000	Flanking Active TSS	Fetal Intestine Large	intestine
24	chr5:58879400-58880000	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr5:58879400-58880600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:58879400-58884000	Active TSS	Brain Substantia Nigra	brain
27	chr5:58879600-58880000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:58879600-58880000	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr5:58879600-58880000	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr5:58879600-58880000	Active TSS	Fetal Kidney	kidney
31	chr5:58879600-58880000	Enhancers	Fetal Muscle Leg	muscle
32	chr5:58879600-58880000	Enhancers	Fetal Stomach	stomach
33	chr5:58879600-58880000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr5:58879600-58880000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr5:58879600-58880000	Flanking Active TSS	Hela-S3	cervix
36	chr5:58879600-58880200	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr5:58879600-58880400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr5:58879600-58880400	Enhancers	Small Intestine	intestine
39	chr5:58879600-58881600	Enhancers	Colon Smooth Muscle	Colon
40	chr5:58879600-58882600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:58879600-58882600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:58879600-58883200	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr5:58879600-58883800	Active TSS	Stomach Mucosa	stomach
44	chr5:58879600-58884200	Active TSS	Colonic Mucosa	Colon
45	chr5:58879600-58884400	Active TSS	Brain Angular Gyrus	brain
46	chr5:58879800-58880000	Enhancers	Aorta	Aorta
47	chr5:58879800-58880200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr5:58879800-58880400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr5:58879800-58880400	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr5:58879800-58880600	Active TSS	Brain Hippocampus Middle	brain

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