Variant report

Variant	rs4806380
Chromosome Location	chr19:37442078-37442079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10404981	0.86[CEU][hapmap]
rs10405984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410594	0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs10411931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412863	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10416960	0.92[ASW][hapmap];0.86[CEU][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs10418314	0.91[YRI][hapmap]
rs10419174	0.88[YRI][hapmap]
rs10419845	0.82[AFR][1000 genomes]
rs10420859	0.84[AFR][1000 genomes]
rs10424100	0.86[AFR][1000 genomes]
rs10424841	0.87[YRI][hapmap]
rs11084873	0.88[YRI][hapmap]
rs12710052	0.80[AMR][1000 genomes]
rs12981965	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs13345489	0.80[AMR][1000 genomes]
rs1624293	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs16971850	0.86[CEU][hapmap]
rs17707101	0.92[ASW][hapmap];0.86[CEU][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28412852	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28495495	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28542490	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28555503	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28608841	0.80[AMR][1000 genomes]
rs28655720	0.80[AMR][1000 genomes]
rs35881914	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3816391	0.85[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4805191	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4805192	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806377	0.89[AFR][1000 genomes]
rs4806383	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806386	0.80[AMR][1000 genomes]
rs62113193	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7249013	0.84[AFR][1000 genomes]
rs8101062	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304878	0.91[LWK][hapmap]
rs997516	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
14	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
16	nsv833818	chr19:37427808-37602800	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
17	nsv579463	chr19:37437106-37488055	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
18	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4806380	ITPKC	cis	cerebellum	SCAN
rs4806380	PAFAH1B3	cis	cerebellum	SCAN
rs4806380	EXOSC5	cis	cerebellum	SCAN
rs4806380	DEDD2	cis	parietal	SCAN
rs4806380	APOC4	cis	cerebellum	SCAN
rs4806380	MEGF8	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37409000-37444800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:37409000-37447400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:37415800-37444600	ZNF genes & repeats	Liver	Liver
4	chr19:37419400-37447400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:37420600-37443000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr19:37420600-37447400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:37420600-37447600	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr19:37430800-37443200	Weak transcription	Pancreas	Pancrea
9	chr19:37435200-37442600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:37435400-37444400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:37437400-37442600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:37437800-37442400	ZNF genes & repeats	Brain Hippocampus Middle	brain
13	chr19:37438200-37442200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:37438200-37442200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
15	chr19:37438200-37442200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
16	chr19:37438200-37442200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
17	chr19:37438200-37442200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr19:37438200-37442200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:37438200-37442200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
20	chr19:37438200-37442400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:37438200-37442400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
22	chr19:37438200-37442400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
23	chr19:37438200-37442400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
24	chr19:37438400-37442400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:37438800-37442400	Weak transcription	Lung	lung
26	chr19:37438800-37442400	ZNF genes & repeats	Osteobl	bone
27	chr19:37438800-37442600	Weak transcription	Esophagus	oesophagus
28	chr19:37439600-37442400	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
29	chr19:37439800-37442200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
30	chr19:37439800-37442400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:37440000-37442600	ZNF genes & repeats	Fetal Brain Female	brain
32	chr19:37440600-37442200	ZNF genes & repeats	Brain Germinal Matrix	brain
33	chr19:37440600-37442600	ZNF genes & repeats	Fetal Brain Male	brain
34	chr19:37441600-37442600	Weak transcription	Aorta	Aorta
35	chr19:37441600-37443400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:37441600-37444800	Weak transcription	Placenta	Placenta
37	chr19:37441600-37446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:37441800-37442200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:37441800-37444600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:37442000-37442400	Strong transcription	HSMM	muscle
41	chr19:37442000-37442600	Weak transcription	Fetal Intestine Large	intestine
42	chr19:37442000-37444000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:37442000-37446800	Weak transcription	Left Ventricle	heart
44	chr19:37442000-37447000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:37442000-37448400	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links