Variant report

Variant	rs3798425
Chromosome Location	chr6:76607550-76607551
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10498904	0.94[CEU][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11753849	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11755704	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11758543	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11967411	0.86[JPT][hapmap]
rs11968058	0.86[JPT][hapmap]
rs12606	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12660330	0.86[JPT][hapmap]
rs12662475	0.84[JPT][hapmap]
rs12662672	0.86[JPT][hapmap]
rs12662718	0.86[JPT][hapmap]
rs12662879	0.86[JPT][hapmap]
rs12663203	0.86[JPT][hapmap]
rs12664049	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664146	0.92[JPT][hapmap]
rs12665404	0.86[JPT][hapmap]
rs1280038	0.94[CEU][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1280040	0.95[CEU][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1280049	0.94[CHB][hapmap];0.94[CHD][hapmap]
rs1280052	0.94[CHB][hapmap];0.94[CHD][hapmap]
rs1280056	0.94[CHB][hapmap]
rs13202519	0.94[CHB][hapmap];0.94[CHD][hapmap];0.80[ASN][1000 genomes]
rs13205059	0.86[JPT][hapmap]
rs1322549	0.80[ASN][1000 genomes]
rs1335043	0.94[CHB][hapmap]
rs17191306	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17192223	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17192279	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17794529	0.88[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17800625	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2104203	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2295936	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2295937	0.86[JPT][hapmap]
rs2748957	0.85[CEU][hapmap]
rs2748963	0.83[EUR][1000 genomes]
rs2748966	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs276695	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs2842541	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2842543	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842545	0.83[AFR][1000 genomes]
rs2842547	0.83[AFR][1000 genomes]
rs3765140	0.89[MEX][hapmap]
rs3778007	0.94[CHB][hapmap];0.94[CHD][hapmap]
rs3778009	0.86[JPT][hapmap]
rs3798426	0.80[ASN][1000 genomes]
rs3798427	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs3798429	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[ASN][1000 genomes]
rs3798433	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798434	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3798435	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3798436	0.86[JPT][hapmap]
rs3798445	0.86[JPT][hapmap]
rs3798450	0.86[JPT][hapmap]
rs3798451	0.86[JPT][hapmap]
rs3818310	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4476795	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs56006932	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57920948	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61237402	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62414787	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62414789	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62414791	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62414798	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62414800	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62414802	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62414803	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62414804	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62414824	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6914716	0.88[CHB][hapmap]
rs6932992	0.94[CHB][hapmap];0.94[CHD][hapmap]
rs72890660	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7742567	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs7748145	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7761004	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7767675	0.80[ASN][1000 genomes]
rs7773977	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9250	1.00[ASW][hapmap];0.84[MEX][hapmap]
rs9343325	0.94[CHB][hapmap]
rs9343327	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs9359141	0.94[CHB][hapmap]
rs9360954	0.94[CHB][hapmap];0.94[CHD][hapmap];0.80[ASN][1000 genomes]
rs9443191	0.86[JPT][hapmap]
rs9443192	0.86[JPT][hapmap]
rs999209	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3798425	SENP6	cis	Whole Blood	GTEx
rs3798425	MYO6	cis	cerebellum	SCAN
rs3798425	MYO6	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:76573000-76624000	Weak transcription	Placenta	Placenta
3	chr6:76573800-76608400	Weak transcription	Esophagus	oesophagus
4	chr6:76574400-76632600	Weak transcription	Spleen	Spleen
5	chr6:76577200-76624600	Weak transcription	Fetal Kidney	kidney
6	chr6:76583800-76624600	Weak transcription	Pancreas	Pancrea
7	chr6:76584200-76608400	Weak transcription	Aorta	Aorta
8	chr6:76584200-76629400	Weak transcription	Ovary	ovary
9	chr6:76584400-76623800	Weak transcription	Lung	lung
10	chr6:76584800-76615200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:76584800-76644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:76585000-76608200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:76585800-76608000	Weak transcription	NH-A	brain
14	chr6:76585800-76624000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:76585800-76624400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:76585800-76626800	Weak transcription	Left Ventricle	heart
17	chr6:76585800-76644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:76586000-76627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:76586200-76624400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:76586400-76607800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:76587600-76623800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:76592600-76624400	Weak transcription	Osteobl	bone
23	chr6:76592800-76631800	Weak transcription	NHEK	skin
24	chr6:76594400-76608400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:76594600-76632200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:76597200-76608400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:76597200-76624600	Weak transcription	Brain Angular Gyrus	brain
28	chr6:76600200-76631800	Weak transcription	HMEC	breast
29	chr6:76600400-76624600	Weak transcription	Brain Substantia Nigra	brain
30	chr6:76600600-76608200	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:76601400-76611600	Weak transcription	Fetal Stomach	stomach
32	chr6:76602400-76619200	Weak transcription	HUVEC	blood vessel
33	chr6:76602600-76624400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:76603600-76619000	Weak transcription	Liver	Liver
35	chr6:76604000-76611800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:76604000-76624400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:76604400-76623800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:76604400-76627000	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:76604600-76623800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:76605600-76614600	Weak transcription	Fetal Intestine Small	intestine
41	chr6:76605800-76608800	Strong transcription	Fetal Intestine Large	intestine
42	chr6:76606200-76623600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:76606400-76608400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:76606600-76607800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:76606600-76615200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:76606600-76623400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:76606600-76623800	Weak transcription	Adipose Nuclei	Adipose
48	chr6:76606600-76628800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:76606600-76629200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:76606600-76632000	Weak transcription	NHDF-Ad	bronchial

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