Variant report

Variant	rs10939895
Chromosome Location	chr5:60567819-60567820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10041973	0.95[ASN][1000 genomes]
rs10052753	0.86[AFR][1000 genomes]
rs10056472	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10075959	0.86[AFR][1000 genomes]
rs10076568	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10079115	0.95[ASN][1000 genomes]
rs10939894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11744226	0.81[AFR][1000 genomes]
rs11745696	0.86[AFR][1000 genomes]
rs11747588	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11750566	0.86[AFR][1000 genomes]
rs11949390	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11960587	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12189420	0.81[ASN][1000 genomes]
rs12696981	0.95[ASN][1000 genomes]
rs12696982	1.00[ASN][1000 genomes]
rs13156118	0.82[ASN][1000 genomes]
rs13167234	0.93[ASN][1000 genomes]
rs13167244	0.93[ASN][1000 genomes]
rs13167246	0.86[ASN][1000 genomes]
rs13179814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13181515	0.86[AFR][1000 genomes]
rs13181517	0.86[AFR][1000 genomes]
rs13183007	0.86[AFR][1000 genomes]
rs13186053	0.81[AFR][1000 genomes]
rs13187871	0.91[ASN][1000 genomes]
rs13190305	0.81[AFR][1000 genomes]
rs13355792	0.95[ASN][1000 genomes]
rs28409386	0.81[AFR][1000 genomes]
rs4235485	0.95[ASN][1000 genomes]
rs4315878	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4379148	0.95[ASN][1000 genomes]
rs4640746	0.85[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs4700415	0.93[ASN][1000 genomes]
rs62366231	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62366234	0.86[ASN][1000 genomes]
rs6449523	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs67749311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72759289	0.90[ASN][1000 genomes]
rs72759299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761408	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7721603	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291707	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60550400-60573400	Weak transcription	Gastric	stomach
2	chr5:60556000-60570200	Weak transcription	HSMM	muscle
3	chr5:60560000-60569200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:60560400-60569400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:60560600-60569000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:60560800-60571200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:60561000-60569000	Weak transcription	Brain Substantia Nigra	brain
8	chr5:60561000-60573200	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:60564600-60570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:60564600-60575400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:60564600-60576000	Weak transcription	Psoas Muscle	Psoas
12	chr5:60565600-60570600	Weak transcription	HUVEC	blood vessel
13	chr5:60565800-60571000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr5:60565800-60571200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr5:60566000-60571200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:60566000-60573200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:60566400-60573000	Weak transcription	Stomach Mucosa	stomach
18	chr5:60566600-60573800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:60567000-60568200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:60567000-60571000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:60567000-60571000	Weak transcription	Lung	lung
22	chr5:60567200-60568600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:60567600-60571200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:60567800-60568200	Weak transcription	NHEK	skin
25	chr5:60567800-60571000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:60567800-60577200	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links