Variant report

Variant	rs324748
Chromosome Location	chr19:53005603-53005604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11084170	0.86[ASN][1000 genomes]
rs11669969	0.85[ASN][1000 genomes]
rs1182867	0.80[AMR][1000 genomes]
rs12610532	0.92[ASN][1000 genomes]
rs12984325	0.87[ASN][1000 genomes]
rs161930	0.85[CEU][hapmap]
rs161932	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1677467	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs172956	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2011702	0.86[ASN][1000 genomes]
rs324745	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs324747	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs326441	0.82[JPT][hapmap]
rs326449	0.82[JPT][hapmap]
rs326452	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs326456	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs326458	0.83[JPT][hapmap]
rs329929	0.85[ASN][1000 genomes]
rs329930	0.83[ASN][1000 genomes]
rs378790	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs389503	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs400278	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs414595	0.97[ASN][1000 genomes]
rs414804	0.87[ASN][1000 genomes]
rs419317	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802968	0.92[ASN][1000 genomes]
rs4802969	0.88[ASN][1000 genomes]
rs4802970	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs621469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs633763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs650885	0.88[ASN][1000 genomes]
rs650937	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666356	0.80[JPT][hapmap]
rs802878	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
8	nsv1058567	chr19:52992455-53021505	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1055825	chr19:53001299-53037378	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs324748	BRSK1	cis	parietal	SCAN
rs324748	ZSCAN18	cis	cerebellum	SCAN
rs324748	ISOC2	cis	cerebellum	SCAN
rs324748	NLRP12	cis	cerebellum	SCAN
rs324748	PPP1R12C	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52997000-53008200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:52997600-53009800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:53000600-53006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:53000800-53005800	Weak transcription	Brain Anterior Caudate	brain
5	chr19:53001000-53006000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr19:53002200-53014200	ZNF genes & repeats	Ovary	ovary
7	chr19:53002600-53021400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:53002800-53006200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:53002800-53010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:53003000-53014800	Weak transcription	Brain Germinal Matrix	brain
11	chr19:53003200-53009600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:53003400-53022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:53003800-53006000	Weak transcription	Brain Hippocampus Middle	brain
14	chr19:53003800-53015000	Weak transcription	Fetal Lung	lung
15	chr19:53003800-53017600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr19:53004000-53009400	ZNF genes & repeats	Lung	lung
17	chr19:53004400-53013000	Strong transcription	Fetal Stomach	stomach
18	chr19:53004400-53014800	Weak transcription	Brain Angular Gyrus	brain
19	chr19:53004600-53014600	Weak transcription	Fetal Brain Male	brain
20	chr19:53004600-53015800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:53004800-53006800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
22	chr19:53004800-53007200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
23	chr19:53004800-53011000	Strong transcription	Right Ventricle	heart
24	chr19:53004800-53012800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:53005000-53006000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:53005000-53006200	Weak transcription	Fetal Intestine Small	intestine
27	chr19:53005000-53006800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:53005200-53006800	Strong transcription	Fetal Brain Female	brain
29	chr19:53005200-53007400	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:53005200-53007600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:53005200-53007600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:53005200-53007600	ZNF genes & repeats	Aorta	Aorta
33	chr19:53005200-53007600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
34	chr19:53005200-53009000	Weak transcription	HSMMtube	muscle
35	chr19:53005200-53009200	ZNF genes & repeats	Spleen	Spleen
36	chr19:53005200-53009400	ZNF genes & repeats	Adipose Nuclei	Adipose
37	chr19:53005200-53010000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr19:53005400-53005800	Strong transcription	Dnd41	blood
39	chr19:53005400-53006600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr19:53005400-53006600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:53005400-53007000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
42	chr19:53005400-53007600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
43	chr19:53005400-53008200	Strong transcription	Fetal Muscle Leg	muscle
44	chr19:53005400-53008400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:53005400-53015800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
46	chr19:53005600-53006200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr19:53005600-53010800	ZNF genes & repeats	Left Ventricle	heart

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