Variant report

Variant	rs26024
Chromosome Location	chr5:127696022-127696023
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs151987	0.92[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs153995	0.98[ASN][1000 genomes]
rs194276	0.90[ASN][1000 genomes]
rs255690	0.92[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs255691	0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs26378	0.82[ASN][1000 genomes]
rs27457	0.90[ASN][1000 genomes]
rs27754	0.94[CHD][hapmap]
rs28114	0.82[CHD][hapmap]
rs32217	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32223	0.82[ASN][1000 genomes]
rs32238	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs331069	0.90[CHB][hapmap];0.94[CHD][hapmap]
rs331071	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs331094	0.81[CHB][hapmap];0.94[CHD][hapmap]
rs331096	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs331098	0.91[YRI][hapmap]
rs331099	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs39941	0.88[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs42281	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs458882	0.92[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs469070	0.88[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs469722	0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][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	nsv599697	chr5:127563563-127731210	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv830483	chr5:127595570-127705124	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs26024	GRAMD3	cis	parietal	SCAN
rs26024	SLC27A6	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127672000-127746000	Weak transcription	NHDF-Ad	bronchial
2	chr5:127673800-127706400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:127675600-127742200	Weak transcription	Fetal Intestine Small	intestine
4	chr5:127677800-127711400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:127678600-127701000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:127679200-127704200	Weak transcription	Fetal Intestine Large	intestine
7	chr5:127679200-127731200	Weak transcription	Right Ventricle	heart
8	chr5:127679800-127704400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:127681400-127704400	Weak transcription	Ovary	ovary
10	chr5:127681400-127706600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:127681600-127704200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:127681600-127714400	Weak transcription	HUVEC	blood vessel
13	chr5:127685400-127725000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:127685600-127704200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:127685800-127702000	Weak transcription	HMEC	breast
16	chr5:127685800-127712400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:127686000-127738400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:127686000-127742000	Weak transcription	A549	lung
19	chr5:127686600-127704800	Weak transcription	NH-A	brain
20	chr5:127686800-127704400	Weak transcription	Left Ventricle	heart
21	chr5:127687600-127704400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:127690200-127696200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:127690200-127698800	Weak transcription	Fetal Stomach	stomach
24	chr5:127690200-127724800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:127691000-127704200	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:127691200-127703600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:127691200-127704200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:127693000-127702600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:127693000-127703800	Weak transcription	NHEK	skin
30	chr5:127693000-127704200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:127693200-127699800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:127693400-127696200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr5:127693400-127697200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:127693400-127698000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:127693400-127698000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:127693400-127698200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:127693400-127699400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:127693400-127714600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:127693800-127696400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:127694200-127696800	Enhancers	Fetal Lung	lung
41	chr5:127694800-127698800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:127695200-127696400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:127695200-127737800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:127695400-127696400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr5:127695400-127697000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:127695400-127701200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:127695600-127703000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:127695800-127697000	Enhancers	Fetal Heart	heart
49	chr5:127695800-127714000	Weak transcription	Fetal Kidney	kidney
50	chr5:127696000-127696600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links