Variant report

Variant	rs11928552
Chromosome Location	chr3:48739883-48739884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 32 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10780033	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs11130176	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs11706983	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11708786	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11713694	0.87[CHD][hapmap]
rs11719291	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11920534	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs11924597	0.92[CEU][hapmap]
rs12493289	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12493578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs12497850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs13434258	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1352420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs17080319	1.00[JPT][hapmap]
rs34037363	0.87[CHD][hapmap]
rs35064573	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3774628	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs3806694	1.00[JPT][hapmap]
rs4858798	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs4858828	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs4858831	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs4974079	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4974085	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4974087	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs6442130	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs6446252	0.92[CEU][hapmap]
rs6446253	0.92[CEU][hapmap]
rs6788650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs6791542	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs7428949	1.00[JPT][hapmap]
rs7430501	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs7431710	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs7431857	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs7616815	0.92[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs7623023	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs7627404	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs7647813	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs7649458	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap]
rs9311430	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs9311432	0.90[CEU][hapmap]
rs9311433	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs9311434	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs9682444	0.92[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs9755490	0.92[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs9811027	1.00[JPT][hapmap]
rs9834996	1.00[JPT][hapmap]
rs9835307	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs9873726	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9876848	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs9882549	0.87[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs11928552	AMT	cis	Muscle Skeletal	GTEx
rs11928552	WDR6	cis	parietal	SCAN
rs11928552	TLR9	cis	parietal	SCAN
rs11928552	NICN1	cis	Thyroid	GTEx
rs11928552	WDR6	cis	cerebellum	SCAN
rs11928552	AMT	cis	Thyroid	GTEx
rs11928552	NCKIPSD	cis	cerebellum	SCAN
rs11928552	WDR6	cis	lymphoblastoid	seeQTL
rs11928552	NCKIPSD	cis	Muscle Skeletal	GTEx
rs11928552	WDR6	cis	Adipose Subcutaneous	GTEx
rs11928552	ZNF589	cis	cerebellum	SCAN
rs11928552	NCKIPSD	cis	lung	GTEx
rs11928552	AMT	cis	parietal	SCAN
rs11928552	ZNF589	cis	parietal	SCAN
rs11928552	WDR6	cis	Muscle Skeletal	GTEx
rs11928552	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11928552	DALRD3	cis	parietal	SCAN
rs11928552	NICN1-AS1	cis	Thyroid	GTEx
rs11928552	P4HTM	cis	parietal	SCAN
rs11928552	NCKIPSD	cis	parietal	SCAN
rs11928552	WDR6	cis	Whole Blood	GTEx
rs11928552	NCKIPSD	cis	Nerve Tibial	GTEx
rs11928552	WDR6	cis	lung	GTEx
rs11928552	C3orf62	cis	cerebellum	SCAN
rs11928552	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs11928552	DALRD3	cis	cerebellum	SCAN
rs11928552	WDR6	cis	Artery Tibial	GTEx
rs11928552	WDR6	cis	Esophagus Mucosa	GTEx
rs11928552	WDR6	cis	Nerve Tibial	GTEx
rs11928552	AMT	cis	cerebellum	SCAN
rs11928552	NCKIPSD	cis	Whole Blood	GTEx
rs11928552	CCDC36	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
2	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
3	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:48725000-48740800	Strong transcription	Dnd41	blood
6	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:48732800-48744800	Weak transcription	Small Intestine	intestine
8	chr3:48732800-48745400	Weak transcription	Psoas Muscle	Psoas
9	chr3:48733000-48740200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:48733000-48744800	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:48733000-48745400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
13	chr3:48733200-48740800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr3:48733200-48744000	Weak transcription	Esophagus	oesophagus
15	chr3:48733200-48746000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:48733200-48746000	Strong transcription	Fetal Intestine Small	intestine
17	chr3:48733200-48746200	Weak transcription	Right Ventricle	heart
18	chr3:48734000-48746400	Weak transcription	Fetal Brain Male	brain
19	chr3:48734200-48740200	Weak transcription	Fetal Heart	heart
20	chr3:48734200-48745400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:48734400-48740200	Weak transcription	NHDF-Ad	bronchial
22	chr3:48734400-48740800	Strong transcription	Fetal Intestine Large	intestine
23	chr3:48734400-48741600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:48734400-48741600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:48734400-48744600	Weak transcription	NHLF	lung
26	chr3:48734400-48745600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:48734400-48746000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:48734400-48746000	Weak transcription	Brain Substantia Nigra	brain
29	chr3:48734400-48746200	Weak transcription	Gastric	stomach
30	chr3:48734400-48746400	Weak transcription	Stomach Mucosa	stomach
31	chr3:48734400-48748800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:48734800-48740800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:48735200-48740600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr3:48735400-48740200	Strong transcription	Fetal Stomach	stomach
35	chr3:48735600-48740200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:48735800-48740400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:48735800-48743000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:48735800-48744000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:48735800-48746000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:48736000-48740000	Strong transcription	Brain Germinal Matrix	brain
41	chr3:48736000-48742000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:48736800-48741800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:48737200-48740000	Weak transcription	Ovary	ovary
44	chr3:48737200-48741600	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:48737200-48741600	Weak transcription	HUVEC	blood vessel
46	chr3:48737200-48742200	Weak transcription	Lung	lung
47	chr3:48737200-48742800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:48737200-48744000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:48737200-48744800	Weak transcription	Fetal Kidney	kidney
50	chr3:48737200-48746200	Weak transcription	Pancreas	Pancrea

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