Variant report

Variant	rs11880056
Chromosome Location	chr19:38252819-38252820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10153500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10407657	0.90[YRI][hapmap]
rs10424047	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10424612	0.90[YRI][hapmap]
rs11878261	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879149	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11880604	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11883255	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];1.00[ASN][1000 genomes]
rs2075282	1.00[JPT][hapmap]
rs2927743	0.81[YRI][hapmap]
rs2927744	0.95[YRI][hapmap]
rs34206817	0.95[AFR][1000 genomes];0.97[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]
rs4802069	0.95[YRI][hapmap]
rs56075341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56264690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56281742	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57504517	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57725815	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57867853	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59966837	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60686304	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108260	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108262	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62108289	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108290	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108292	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108293	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108297	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62108350	0.95[ASN][1000 genomes]
rs62108354	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110178	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110185	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110186	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110187	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110188	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62111488	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62111490	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246147	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7247175	1.00[EUR][1000 genomes]
rs7247345	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7255283	0.90[YRI][hapmap]
rs7258992	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259029	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259272	0.88[CHB][hapmap]
rs7259717	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930999	0.83[EUR][1000 genomes]
rs73932929	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73932955	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101476	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8101991	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102189	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8104124	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104747	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8108261	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8113076	0.90[YRI][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	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

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38230800-38259800	Weak transcription	Fetal Thymus	thymus
2	chr19:38231000-38258200	Weak transcription	Brain Anterior Caudate	brain
3	chr19:38231000-38258400	Weak transcription	Fetal Kidney	kidney
4	chr19:38231000-38258800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:38231000-38260400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:38231400-38255800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr19:38231400-38259400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:38231400-38259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:38231800-38253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:38231800-38257600	Weak transcription	HSMM	muscle
11	chr19:38231800-38258200	Weak transcription	HSMMtube	muscle
12	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
13	chr19:38232200-38253000	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:38232400-38253600	Weak transcription	Right Ventricle	heart
15	chr19:38232400-38254000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:38232400-38255600	Weak transcription	Psoas Muscle	Psoas
17	chr19:38232400-38256600	Weak transcription	Dnd41	blood
18	chr19:38235200-38253200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
20	chr19:38237000-38260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:38238800-38253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:38238800-38253200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:38238800-38254000	Weak transcription	Fetal Brain Female	brain
24	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
25	chr19:38239000-38253600	Weak transcription	Fetal Intestine Large	intestine
26	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
27	chr19:38239400-38256600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr19:38239400-38257400	Weak transcription	Brain Angular Gyrus	brain
29	chr19:38242200-38258400	Weak transcription	NHDF-Ad	bronchial
30	chr19:38242800-38269000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:38243000-38258200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:38243600-38253400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:38243600-38257200	Weak transcription	Fetal Lung	lung
34	chr19:38245200-38258200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:38246200-38258400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:38246800-38259600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:38246800-38259800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr19:38247400-38258200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr19:38247400-38259800	Weak transcription	Placenta	Placenta
40	chr19:38247800-38253000	Weak transcription	Left Ventricle	heart
41	chr19:38247800-38260000	Weak transcription	Osteobl	bone
42	chr19:38247800-38269200	Weak transcription	Hela-S3	cervix
43	chr19:38248400-38264600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:38248800-38269400	Weak transcription	NH-A	brain
45	chr19:38249000-38254200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr19:38249000-38259000	Weak transcription	Thymus	Thymus
47	chr19:38249200-38254800	ZNF genes & repeats	Liver	Liver
48	chr19:38249200-38269000	Weak transcription	Spleen	Spleen
49	chr19:38249400-38258200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr19:38249800-38253600	Weak transcription	Fetal Intestine Small	intestine

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