Variant report

Variant	rs438605
Chromosome Location	chr19:53008561-53008562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2615575	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs329927	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs329928	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs329931	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs329938	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs444461	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs636090	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs672635	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs810620	0.93[AFR][1000 genomes];1.00[AMR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52997600-53009800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr19:53002200-53014200	ZNF genes & repeats	Ovary	ovary
3	chr19:53002600-53021400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:53002800-53010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:53003000-53014800	Weak transcription	Brain Germinal Matrix	brain
6	chr19:53003200-53009600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:53003400-53022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:53003800-53015000	Weak transcription	Fetal Lung	lung
9	chr19:53003800-53017600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr19:53004000-53009400	ZNF genes & repeats	Lung	lung
11	chr19:53004400-53013000	Strong transcription	Fetal Stomach	stomach
12	chr19:53004400-53014800	Weak transcription	Brain Angular Gyrus	brain
13	chr19:53004600-53014600	Weak transcription	Fetal Brain Male	brain
14	chr19:53004600-53015800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:53004800-53011000	Strong transcription	Right Ventricle	heart
16	chr19:53004800-53012800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:53005200-53009000	Weak transcription	HSMMtube	muscle
18	chr19:53005200-53009200	ZNF genes & repeats	Spleen	Spleen
19	chr19:53005200-53009400	ZNF genes & repeats	Adipose Nuclei	Adipose
20	chr19:53005200-53010000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr19:53005400-53015800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:53005600-53010800	ZNF genes & repeats	Left Ventricle	heart
23	chr19:53005800-53010800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:53005800-53014000	Weak transcription	Dnd41	blood
25	chr19:53006400-53009000	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:53006400-53021200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:53006400-53021400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:53006600-53009200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:53006600-53009400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:53006600-53009600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:53006600-53014400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:53006600-53014800	Weak transcription	Brain Anterior Caudate	brain
33	chr19:53006600-53015600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:53006600-53016200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:53006800-53015000	Weak transcription	Fetal Brain Female	brain
36	chr19:53006800-53021400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:53007000-53015000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:53007000-53021400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr19:53007200-53009200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr19:53007400-53009000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:53007400-53015200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr19:53007600-53008800	Weak transcription	Aorta	Aorta
43	chr19:53007600-53010400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:53008000-53009000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:53008200-53008800	Weak transcription	Fetal Muscle Leg	muscle
46	chr19:53008200-53010400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr19:53008200-53011600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:53008400-53010400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:53008400-53013200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:53008400-53015600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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