Variant report

Variant	rs57867853
Chromosome Location	chr19:38239942-38239943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10153500	0.97[EUR][1000 genomes]
rs10424047	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11878261	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879149	0.91[EUR][1000 genomes]
rs11880056	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880604	0.91[EUR][1000 genomes]
rs11883255	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34206817	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743484	0.88[EUR][1000 genomes]
rs45505797	0.83[EUR][1000 genomes]
rs56075341	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56264690	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56281742	1.00[EUR][1000 genomes]
rs57504517	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57725815	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59966837	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60686304	1.00[EUR][1000 genomes]
rs62108260	1.00[EUR][1000 genomes]
rs62108262	0.91[EUR][1000 genomes]
rs62108289	1.00[EUR][1000 genomes]
rs62108290	1.00[EUR][1000 genomes]
rs62108292	1.00[EUR][1000 genomes]
rs62108293	1.00[EUR][1000 genomes]
rs62108297	1.00[EUR][1000 genomes]
rs62108348	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62108350	0.95[ASN][1000 genomes]
rs62108354	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110178	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110183	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110185	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110186	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110187	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110188	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62111488	1.00[EUR][1000 genomes]
rs62111490	1.00[EUR][1000 genomes]
rs7245981	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246147	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7247175	1.00[EUR][1000 genomes]
rs7247345	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7258992	1.00[EUR][1000 genomes]
rs7259029	1.00[EUR][1000 genomes]
rs7259717	1.00[EUR][1000 genomes]
rs73930999	0.83[EUR][1000 genomes]
rs73932929	1.00[EUR][1000 genomes]
rs73932955	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101476	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8101991	1.00[EUR][1000 genomes]
rs8102189	1.00[EUR][1000 genomes]
rs8104124	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104747	1.00[EUR][1000 genomes]
rs8108261	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3321680	chr19:38239812-38244210	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38221200-38241800	ZNF genes & repeats	Liver	Liver
2	chr19:38224600-38241600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:38230800-38251400	Weak transcription	Pancreas	Pancrea
4	chr19:38230800-38252600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:38230800-38259800	Weak transcription	Fetal Thymus	thymus
6	chr19:38231000-38246600	Weak transcription	Left Ventricle	heart
7	chr19:38231000-38246800	Weak transcription	Brain Germinal Matrix	brain
8	chr19:38231000-38250400	Weak transcription	Brain Substantia Nigra	brain
9	chr19:38231000-38258200	Weak transcription	Brain Anterior Caudate	brain
10	chr19:38231000-38258400	Weak transcription	Fetal Kidney	kidney
11	chr19:38231000-38258800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:38231000-38260400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:38231400-38250600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr19:38231400-38255800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:38231400-38259400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:38231400-38259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:38231800-38245800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:38231800-38253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:38231800-38257600	Weak transcription	HSMM	muscle
20	chr19:38231800-38258200	Weak transcription	HSMMtube	muscle
21	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
22	chr19:38232200-38250600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr19:38232200-38253000	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:38232400-38242800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:38232400-38243200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr19:38232400-38252000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr19:38232400-38253600	Weak transcription	Right Ventricle	heart
28	chr19:38232400-38254000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:38232400-38255600	Weak transcription	Psoas Muscle	Psoas
30	chr19:38232400-38256600	Weak transcription	Dnd41	blood
31	chr19:38235200-38250600	Weak transcription	Gastric	stomach
32	chr19:38235200-38253200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:38235400-38251400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:38235400-38252800	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:38235600-38250800	Weak transcription	Fetal Stomach	stomach
36	chr19:38235600-38251400	Weak transcription	Fetal Muscle Leg	muscle
37	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
38	chr19:38236600-38249000	Weak transcription	Fetal Intestine Small	intestine
39	chr19:38236600-38250400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:38236600-38250400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:38236800-38243200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:38237000-38241600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr19:38237000-38260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:38237200-38240000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
45	chr19:38237400-38242800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr19:38237400-38252600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:38237400-38252800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:38237600-38243200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:38237800-38246800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:38238000-38240400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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