Variant report

Variant	rs16889892
Chromosome Location	chr5:58778376-58778377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1156028	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12518641	0.85[JPT][hapmap]
rs1551564	0.85[JPT][hapmap]
rs16877169	0.86[EUR][1000 genomes]
rs16889853	0.81[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs16889865	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16889878	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs174039	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17728654	0.83[EUR][1000 genomes]
rs17795596	0.89[CEU][hapmap]
rs17796040	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs17796399	0.84[EUR][1000 genomes]
rs1824154	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1902610	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2081092	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs2112910	0.85[JPT][hapmap]
rs35450986	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852147	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41447947	0.85[JPT][hapmap]
rs4604141	0.84[EUR][1000 genomes]
rs6450519	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs6870632	0.81[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs73097356	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7704141	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7729912	0.84[EUR][1000 genomes]
rs7738023	0.91[EUR][1000 genomes]
rs988827	0.90[ASN][1000 genomes]
rs988828	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.89[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	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	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
4	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv881707	chr5:58741491-58784102	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58754600-58780200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:58762000-58778800	Weak transcription	Aorta	Aorta
3	chr5:58762600-58780600	Weak transcription	Fetal Lung	lung
4	chr5:58768800-58779400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:58770200-58779400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:58774000-58783600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:58774600-58783000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:58774800-58779000	Genic enhancers	A549	lung
9	chr5:58775000-58778800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:58775200-58778800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:58775200-58780200	Weak transcription	Brain Substantia Nigra	brain
12	chr5:58775400-58779400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:58775400-58779400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:58775400-58779600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:58775600-58780400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:58775800-58779400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:58776600-58783000	Weak transcription	Fetal Intestine Large	intestine
18	chr5:58777000-58778800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:58777400-58783600	Weak transcription	Psoas Muscle	Psoas
20	chr5:58777800-58781600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:58778000-58778600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr5:58778000-58780000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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