Variant report

Variant	rs6462022
Chromosome Location	chr7:27556589-27556590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1005418	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10486549	0.86[JPT][hapmap]
rs12234338	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12667470	0.86[JPT][hapmap]
rs12670250	0.91[JPT][hapmap]
rs12671723	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12674175	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12700831	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs1524527	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs16874305	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17155443	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17155465	0.80[CEU][hapmap]
rs17155498	0.91[JPT][hapmap]
rs17155505	0.91[JPT][hapmap]
rs17155537	0.86[JPT][hapmap]
rs2391437	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2391450	0.91[JPT][hapmap]
rs2893292	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs34536886	0.85[EUR][1000 genomes]
rs3735570	1.00[CHB][hapmap]
rs42089	1.00[JPT][hapmap]
rs6462023	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6975900	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs759268	0.91[JPT][hapmap]
rs759272	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs7778454	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7779488	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs999491	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830930	chr7:27395838-27587355	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6462022	HIBADH	cis	parietal	SCAN
rs6462022	TRA2A	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27539400-27558000	Weak transcription	Fetal Stomach	stomach
2	chr7:27549200-27561200	Weak transcription	Liver	Liver
3	chr7:27550600-27563400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:27551200-27563800	Weak transcription	Left Ventricle	heart
5	chr7:27551600-27563800	Weak transcription	Placenta	Placenta
6	chr7:27552600-27564800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:27552600-27568200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:27552800-27557000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:27553000-27563600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:27553200-27581000	Weak transcription	Fetal Heart	heart
11	chr7:27553600-27557000	Weak transcription	Primary T cells from cord blood	blood
12	chr7:27553600-27564000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:27553800-27564600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:27554400-27564000	Weak transcription	K562	blood
15	chr7:27554800-27558000	Weak transcription	HepG2	liver
16	chr7:27554800-27558200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:27555000-27568600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:27555400-27557200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr7:27555600-27556600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr7:27555600-27556600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:27555600-27556800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr7:27555600-27557000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr7:27555800-27581000	Weak transcription	Gastric	stomach
24	chr7:27556000-27556600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr7:27556000-27562800	Weak transcription	Aorta	Aorta
26	chr7:27556000-27563800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:27556000-27579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:27556000-27581600	Weak transcription	HMEC	breast
29	chr7:27556200-27556600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
30	chr7:27556200-27556600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr7:27556200-27556600	Enhancers	Fetal Kidney	kidney
32	chr7:27556200-27556800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
33	chr7:27556200-27557600	Weak transcription	Fetal Lung	lung
34	chr7:27556200-27564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:27556400-27556600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:27556400-27556600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
37	chr7:27556400-27557000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
38	chr7:27556400-27557200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
39	chr7:27556400-27564400	Weak transcription	Brain Substantia Nigra	brain
40	chr7:27556400-27584400	Weak transcription	NHEK	skin
41	chr7:27556400-27586400	Weak transcription	H9 Cell Line	embryonic stem cell

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