Variant report

Variant	rs413061
Chromosome Location	chr19:44466754-44466755
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10402944	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2299936	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2429734	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs364278	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs366431	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs368492	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs376655	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs377931	0.88[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs377934	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs381220	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs381872	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs383133	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs385202	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs385578	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs386249	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs386747	0.85[AMR][1000 genomes]
rs388547	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs390134	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs391961	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs394132	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs394380	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs395419	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs396188	0.92[CEU][hapmap];0.80[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs397276	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs400591	0.92[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs401770	0.92[CEU][hapmap];0.80[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs415468	0.88[EUR][1000 genomes]
rs415867	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs418336	0.96[CEU][hapmap]
rs424041	0.92[CEU][hapmap];0.80[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs427401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429611	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437700	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs439417	0.92[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs441386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs441742	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs442543	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs442903	0.82[ASN][1000 genomes]
rs444816	0.92[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs445865	0.86[AMR][1000 genomes]
rs453682	0.92[CHB][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs453932	0.91[CHD][hapmap];0.81[JPT][hapmap]
rs454376	0.89[GIH][hapmap];0.85[AMR][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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv912109	chr19:44459074-44493142	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs413061	KLC3	cis	parietal	SCAN
rs413061	ZNF155	cis	multi-tissue	Pritchard
rs413061	VSIG10L	cis	parietal	SCAN
rs413061	FTL	cis	cerebellum	SCAN
rs413061	FOXA3	cis	cerebellum	SCAN
rs413061	CYTH2	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44456200-44476600	ZNF genes & repeats	Brain Germinal Matrix	brain
2	chr19:44456400-44479600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:44456400-44487800	ZNF genes & repeats	Liver	Liver
4	chr19:44456600-44475200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:44460000-44467400	Weak transcription	HSMM	muscle
6	chr19:44461800-44475200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:44462000-44475000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:44462000-44485200	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:44462200-44474800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
10	chr19:44462200-44475600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:44462200-44475800	ZNF genes & repeats	Fetal Lung	lung
12	chr19:44462200-44476600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr19:44462400-44475400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
14	chr19:44462800-44475400	ZNF genes & repeats	Brain Anterior Caudate	brain
15	chr19:44463000-44478800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:44463200-44475600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr19:44463200-44475600	ZNF genes & repeats	Brain Hippocampus Middle	brain
18	chr19:44463400-44476400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:44463600-44466800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:44463600-44466800	Weak transcription	Fetal Kidney	kidney
21	chr19:44463600-44467600	Weak transcription	Osteobl	bone
22	chr19:44464000-44475000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:44464400-44475800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
24	chr19:44465000-44467400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr19:44465200-44466800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr19:44465200-44468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:44465400-44466800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:44465400-44466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:44465400-44466800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:44465400-44466800	Weak transcription	Gastric	stomach
31	chr19:44465400-44467400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:44465400-44468400	Weak transcription	Lung	lung
33	chr19:44465400-44468400	Weak transcription	Pancreas	Pancrea
34	chr19:44465400-44468400	Weak transcription	Right Ventricle	heart
35	chr19:44465600-44466800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:44465600-44467000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:44465600-44468400	Weak transcription	Placenta	Placenta
38	chr19:44465600-44468800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr19:44465600-44469000	Weak transcription	Fetal Stomach	stomach
40	chr19:44465600-44475400	ZNF genes & repeats	Fetal Brain Male	brain
41	chr19:44465800-44475400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:44466200-44473200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:44466200-44475000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:44466200-44475200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:44466200-44475600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
46	chr19:44466400-44467000	ZNF genes & repeats	Left Ventricle	heart
47	chr19:44466400-44467200	ZNF genes & repeats	Aorta	Aorta
48	chr19:44466400-44474800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:44466400-44474800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
50	chr19:44466400-44474800	ZNF genes & repeats	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links