Variant report

Variant	rs381872
Chromosome Location	chr19:44466156-44466157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10402944	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2299936	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2429734	0.90[EUR][1000 genomes]
rs364278	0.96[CEU][hapmap]
rs366431	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs376655	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs377931	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs377934	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs381220	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs383133	0.84[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs385202	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs385578	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs386249	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs388547	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs390134	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs391961	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs394132	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs394380	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs395419	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs396188	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs397276	0.92[CEU][hapmap]
rs400591	0.92[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs401770	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs413061	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]
rs415468	0.86[EUR][1000 genomes]
rs415867	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs418336	0.96[CEU][hapmap]
rs424041	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs427401	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs429611	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs437700	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs439417	0.92[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs441386	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs441742	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs442543	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs444816	0.92[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs445865	0.81[AMR][1000 genomes]
rs453932	0.81[JPT][hapmap]
rs454376	0.82[GIH][hapmap]
rs47775	0.80[YRI][hapmap]
rs8099924	0.87[MEX][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs381872	KLC3	cis	parietal	SCAN
rs381872	VSIG10L	cis	parietal	SCAN
rs381872	FTL	cis	cerebellum	SCAN
rs381872	CYTH2	cis	parietal	SCAN
rs381872	FOXA3	cis	cerebellum	SCAN

Chromatin state (count:55 , 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	chr19:44456800-44466200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:44460000-44467400	Weak transcription	HSMM	muscle
7	chr19:44461800-44475200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr19:44462000-44475000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:44462000-44485200	ZNF genes & repeats	Adipose Nuclei	Adipose
10	chr19:44462200-44474800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
11	chr19:44462200-44475600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:44462200-44475800	ZNF genes & repeats	Fetal Lung	lung
13	chr19:44462200-44476600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
14	chr19:44462400-44475400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr19:44462800-44475400	ZNF genes & repeats	Brain Anterior Caudate	brain
16	chr19:44463000-44478800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:44463200-44475600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr19:44463200-44475600	ZNF genes & repeats	Brain Hippocampus Middle	brain
19	chr19:44463400-44476400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:44463600-44466800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:44463600-44466800	Weak transcription	Fetal Kidney	kidney
22	chr19:44463600-44467600	Weak transcription	Osteobl	bone
23	chr19:44464000-44475000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:44464400-44475800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr19:44465000-44467400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:44465200-44466800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr19:44465200-44468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:44465400-44466200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:44465400-44466200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr19:44465400-44466400	Weak transcription	Aorta	Aorta
31	chr19:44465400-44466400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:44465400-44466400	Weak transcription	Left Ventricle	heart
33	chr19:44465400-44466800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:44465400-44466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:44465400-44466800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:44465400-44466800	Weak transcription	Gastric	stomach
37	chr19:44465400-44467400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:44465400-44468400	Weak transcription	Lung	lung
39	chr19:44465400-44468400	Weak transcription	Pancreas	Pancrea
40	chr19:44465400-44468400	Weak transcription	Right Ventricle	heart
41	chr19:44465600-44466400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:44465600-44466400	Weak transcription	Ovary	ovary
43	chr19:44465600-44466600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr19:44465600-44466600	Weak transcription	Brain Substantia Nigra	brain
45	chr19:44465600-44466600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:44465600-44466600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:44465600-44466800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:44465600-44467000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:44465600-44468400	Weak transcription	Placenta	Placenta
50	chr19:44465600-44468800	Weak transcription	Primary monocytes fromperipheralblood	blood

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