Variant report

Variant	rs247938
Chromosome Location	chr5:99898851-99898852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10038896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1457766	0.88[ASN][1000 genomes]
rs247939	0.84[CHD][hapmap]
rs247940	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs247942	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs258542	0.81[ASN][1000 genomes]
rs26026	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs26027	0.81[CHD][hapmap];0.89[GIH][hapmap];0.80[ASN][1000 genomes]
rs26029	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs393100	0.92[ASN][1000 genomes]
rs425172	0.92[ASN][1000 genomes]
rs574689	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs6860018	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv882461	chr5:99745767-99927338	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv882462	chr5:99745767-100060150	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1025890	chr5:99745775-99936186	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv882463	chr5:99784116-99898851	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv882464	chr5:99784116-99905367	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv882465	chr5:99784116-99927338	Flanking Active TSS Enhancers Strong transcription Weak transcription 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	13 gene(s)	inside rSNPs	diseases
12	nsv1018395	chr5:99827242-100003207	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv2763473	chr5:99883352-99907664	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv818363	chr5:99898851-99906222	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99872400-99931400	Weak transcription	Aorta	Aorta
2	chr5:99872600-99922800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:99872800-99902000	Weak transcription	HSMM	muscle
4	chr5:99872800-99916200	Weak transcription	Ovary	ovary
5	chr5:99873400-99916200	Weak transcription	Fetal Stomach	stomach
6	chr5:99873400-99930600	Weak transcription	NH-A	brain
7	chr5:99878400-99930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:99882200-99899200	Weak transcription	Left Ventricle	heart
9	chr5:99884000-99910400	Weak transcription	HUVEC	blood vessel
10	chr5:99886800-99899400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr5:99886800-99930200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:99887200-99912000	Weak transcription	Psoas Muscle	Psoas
13	chr5:99887200-99916200	Weak transcription	Lung	lung
14	chr5:99887200-99924600	Weak transcription	Fetal Thymus	thymus
15	chr5:99887600-99899600	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:99887600-99907200	Weak transcription	Pancreas	Pancrea
17	chr5:99893800-99910400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:99894400-99907400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:99894800-99899400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr5:99895000-99899000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:99895400-99902000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:99895400-99919800	Weak transcription	HSMMtube	muscle
23	chr5:99895600-99903000	Weak transcription	Placenta	Placenta
24	chr5:99895800-99911600	Weak transcription	NHDF-Ad	bronchial
25	chr5:99895800-99921000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:99895800-99931000	Weak transcription	Fetal Intestine Large	intestine
27	chr5:99896200-99916200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:99896200-99927600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:99896400-99899000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:99896400-99899000	Weak transcription	Liver	Liver
31	chr5:99896400-99903600	Weak transcription	Fetal Kidney	kidney
32	chr5:99896600-99933800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr5:99896800-99902400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:99896800-99903000	Weak transcription	Osteobl	bone
35	chr5:99896800-99931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:99897000-99902200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:99897000-99902400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:99897000-99928800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:99897200-99910200	Weak transcription	Colon Smooth Muscle	Colon
40	chr5:99897200-99923800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:99897400-99902600	Weak transcription	Brain Substantia Nigra	brain
42	chr5:99897600-99899800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:99897600-99900200	Strong transcription	Primary B cells from cord blood	blood
44	chr5:99897600-99900200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr5:99897800-99899600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:99897800-99899800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:99897800-99899800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:99897800-99899800	Strong transcription	Adipose Nuclei	Adipose
49	chr5:99897800-99899800	Strong transcription	Fetal Lung	lung
50	chr5:99897800-99899800	Strong transcription	GM12878-XiMat	blood

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