Variant report

Variant	rs9831648
Chromosome Location	chr3:49214303-49214304
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49158589..49160627-chr3:49212099..49214336,2	K562	blood:
2	chr3:49210124..49211689-chr3:49213710..49215356,2	K562	blood:
3	chr3:49210124..49212449-chr3:49213139..49215737,4	K562	blood:
4	chr3:49201068..49204007-chr3:49213052..49215729,2	K562	blood:
5	chr3:49207629..49210061-chr3:49211282..49215140,3	MCF-7	breast:
6	chr3:49131687..49134642-chr3:49213919..49216265,2	K562	blood:

Variant related genes	Relation type
ENSG00000198218	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000185909	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10154992	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs11130181	0.84[AFR][1000 genomes]
rs11130183	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	0.81[ASW][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs13084037	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082923	1.00[ASN][1000 genomes]
rs2099526	1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs3212	0.86[YRI][hapmap]
rs3448	1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs35713889	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4292260	0.87[ASW][hapmap];0.98[LWK][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4384984	1.00[ASN][1000 genomes]
rs4521268	0.82[YRI][hapmap]
rs4955411	0.87[ASW][hapmap];0.98[LWK][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955416	0.87[ASW][hapmap];0.95[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4955417	1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap]
rs4955421	0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955439	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955443	1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs4974080	0.86[YRI][hapmap]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs6446205	0.89[YRI][hapmap]
rs6446256	0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6778080	1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6779394	0.93[YRI][hapmap]
rs6781790	0.82[YRI][hapmap]
rs6785045	1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6808036	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs6809851	1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs73088137	1.00[ASN][1000 genomes]
rs7429661	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432989	0.93[YRI][hapmap]
rs7617480	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619016	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7621015	0.82[YRI][hapmap]
rs7626076	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7626445	0.82[YRI][hapmap]
rs7631586	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9586	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974495	1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs9817807	1.00[ASN][1000 genomes]
rs9834003	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840050	0.86[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9846123	0.82[YRI][hapmap]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9865051	0.82[TSI][hapmap]
rs9867285	1.00[ASN][1000 genomes]
rs9881860	1.00[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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs9831648	SEMA3G	cis	cerebellum	SCAN
rs9831648	WDR6	cis	parietal	SCAN
rs9831648	AMT	cis	cerebellum	SCAN
rs9831648	DALRD3	cis	cerebellum	SCAN
rs9831648	WDR6	cis	Muscle Skeletal	GTEx
rs9831648	WDR6	cis	Heart Left Ventricle	GTEx
rs9831648	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs9831648	ZNF589	cis	parietal	SCAN
rs9831648	WDR6	cis	lung	GTEx
rs9831648	AMT	cis	Nerve Tibial	GTEx
rs9831648	NICN1	cis	Thyroid	GTEx
rs9831648	AMT	cis	Whole Blood	GTEx
rs9831648	GPX1	cis	parietal	SCAN
rs9831648	NICN1	cis	cerebellum	SCAN
rs9831648	AMT	cis	Thyroid	GTEx
rs9831648	QRICH1	cis	cerebellum	SCAN
rs9831648	GMPPB	cis	parietal	SCAN
rs9831648	AMT	cis	lymphoblastoid	seeQTL
rs9831648	WDR6	cis	cerebellum	SCAN
rs9831648	GNL3	cis	cerebellum	SCAN
rs9831648	DALRD3	cis	parietal	SCAN
rs9831648	AMT	cis	parietal	SCAN
rs9831648	P4HTM	cis	parietal	SCAN
rs9831648	NME6	cis	cerebellum	SCAN
rs9831648	GNL3	cis	parietal	SCAN
rs9831648	NICN1-AS1	cis	Thyroid	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49209800-49215000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49210800-49214600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:49211000-49215200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:49211200-49214600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:49211200-49218800	Weak transcription	Fetal Kidney	kidney
6	chr3:49211200-49224600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:49211400-49214400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:49211400-49214400	Genic enhancers	Left Ventricle	heart
9	chr3:49211400-49215000	Weak transcription	NHDF-Ad	bronchial
10	chr3:49211400-49216000	Weak transcription	Brain Substantia Nigra	brain
11	chr3:49211400-49217600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:49211600-49214400	Strong transcription	Esophagus	oesophagus
13	chr3:49211600-49214800	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr3:49211600-49215200	Genic enhancers	Adipose Nuclei	Adipose
15	chr3:49211800-49214400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:49211800-49214800	Weak transcription	K562	blood
17	chr3:49211800-49215000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:49211800-49215000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:49211800-49215000	Genic enhancers	Right Ventricle	heart
20	chr3:49211800-49216000	Genic enhancers	Fetal Muscle Trunk	muscle
21	chr3:49211800-49216200	Genic enhancers	Fetal Muscle Leg	muscle
22	chr3:49211800-49216600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:49212000-49214400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
24	chr3:49212000-49215200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:49212000-49215400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:49212000-49216200	Weak transcription	Osteobl	bone
27	chr3:49212200-49214400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:49212200-49214600	Strong transcription	Placenta	Placenta
29	chr3:49212200-49214800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:49212200-49218800	Weak transcription	HepG2	liver
31	chr3:49212400-49214800	Strong transcription	Fetal Lung	lung
32	chr3:49212400-49215200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:49212400-49215400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:49212400-49215600	Strong transcription	Lung	lung
35	chr3:49212600-49214600	Weak transcription	Fetal Brain Male	brain
36	chr3:49212600-49216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:49212800-49214400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:49212800-49214400	Strong transcription	Rectal Smooth Muscle	rectum
39	chr3:49212800-49215200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:49212800-49215600	Strong transcription	Aorta	Aorta
41	chr3:49212800-49215800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:49212800-49216200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:49212800-49217000	Strong transcription	Fetal Stomach	stomach
44	chr3:49213000-49215400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr3:49213000-49217200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:49213200-49215000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:49213200-49215200	Strong transcription	Fetal Intestine Large	intestine
48	chr3:49213200-49215800	Strong transcription	Spleen	Spleen
49	chr3:49213400-49216000	Strong transcription	Fetal Intestine Small	intestine
50	chr3:49213400-49217600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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