Variant report

Variant	rs10040956
Chromosome Location	chr5:178299188-178299189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10035887	0.86[EUR][1000 genomes]
rs10067521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077950	0.83[CHB][hapmap]
rs1046726	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10479515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516151	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs11249603	0.84[EUR][1000 genomes]
rs11743869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746382	0.83[EUR][1000 genomes]
rs11955586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960446	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655480	0.83[CHB][hapmap]
rs12658098	0.83[CHB][hapmap]
rs13154558	0.86[EUR][1000 genomes]
rs1496949	0.88[CEU][hapmap]
rs1496950	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs1995079	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs4130052	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700927	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs62393052	0.88[EUR][1000 genomes]
rs6600990	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6866021	0.86[EUR][1000 genomes]
rs6870709	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872605	0.86[EUR][1000 genomes]
rs6872794	0.85[EUR][1000 genomes]
rs6873993	0.86[EUR][1000 genomes]
rs6877198	0.84[CHB][hapmap]
rs6885597	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891035	0.84[CHB][hapmap]
rs7445694	0.83[CHB][hapmap]
rs7446225	0.83[CHB][hapmap]
rs7447547	0.83[CHB][hapmap]
rs7701607	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs7702579	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7702879	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs9329059	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv462574	chr5:178269682-178313078	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv600463	chr5:178269682-178313078	Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr5:178288400-178299200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr5:178288600-178299400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:178288800-178300000	Strong transcription	Fetal Lung	lung
6	chr5:178288800-178302200	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:178289000-178299600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:178289000-178301000	Strong transcription	Fetal Muscle Leg	muscle
10	chr5:178289000-178301600	Weak transcription	Stomach Mucosa	stomach
11	chr5:178289400-178302200	Strong transcription	Brain Anterior Caudate	brain
12	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:178289800-178300200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:178289800-178300200	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr5:178290000-178299400	Weak transcription	Fetal Heart	heart
16	chr5:178290000-178302200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:178290600-178299600	Strong transcription	Brain Germinal Matrix	brain
18	chr5:178290600-178299800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:178290600-178301200	Strong transcription	Brain Cingulate Gyrus	brain
20	chr5:178290800-178300200	Strong transcription	Left Ventricle	heart
21	chr5:178291000-178299200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr5:178291000-178299200	Strong transcription	Fetal Thymus	thymus
23	chr5:178291000-178300000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
25	chr5:178291400-178300200	Strong transcription	Dnd41	blood
26	chr5:178292000-178303000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:178292200-178299200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:178292200-178302200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:178292600-178299200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:178292600-178299400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr5:178292600-178299400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:178292600-178299600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:178292600-178300200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr5:178292600-178300200	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr5:178292600-178300600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr5:178292600-178301200	Strong transcription	Osteobl	bone
37	chr5:178292600-178305000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:178292600-178305200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr5:178292800-178301400	Strong transcription	Rectal Smooth Muscle	rectum
40	chr5:178293000-178299200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:178293000-178299600	Strong transcription	Brain Angular Gyrus	brain
42	chr5:178293000-178300000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr5:178293400-178301000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr5:178294200-178301400	Weak transcription	Hela-S3	cervix
45	chr5:178294800-178300400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:178295000-178300400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:178295800-178299200	Strong transcription	NH-A	brain
48	chr5:178295800-178299400	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr5:178295800-178300000	Strong transcription	NHDF-Ad	bronchial
50	chr5:178296000-178299200	ZNF genes & repeats	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links