Variant report

Variant	rs353409
Chromosome Location	chr19:38443559-38443560
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38441551..38443321-chr19:38443505..38445243,2	K562	blood:
2	chr19:38432664..38434680-chr19:38442017..38444946,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10422056	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11083438	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11083439	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11668384	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12462485	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12610891	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1632177	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643464	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643465	0.85[CEU][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643472	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725468	0.85[EUR][1000 genomes]
rs1725486	0.95[ASN][1000 genomes]
rs1725490	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17306795	0.90[CHB][hapmap]
rs241937	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs241940	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs241941	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs241942	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs241943	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs241944	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs241946	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs241948	1.00[CHB][hapmap]
rs241951	0.90[CHB][hapmap]
rs353405	0.96[EUR][1000 genomes]
rs353406	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353412	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs353413	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3894129	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4802134	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4803536	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4803566	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6508748	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6508752	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs697433	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250668	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7254828	1.00[CHB][hapmap]
rs7255551	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8102871	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8103882	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8105694	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8110417	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8111400	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs833915	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs833916	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs856302	1.00[CHB][hapmap]
rs856309	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs861308	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	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
2	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38423600-38444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:38424800-38444000	Weak transcription	NHDF-Ad	bronchial
3	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
4	chr19:38426400-38444000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:38426600-38450800	Weak transcription	Ovary	ovary
7	chr19:38426800-38443800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:38427000-38444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:38427000-38444000	Weak transcription	Fetal Brain Female	brain
10	chr19:38427200-38443800	Weak transcription	NHEK	skin
11	chr19:38427200-38444200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:38427400-38443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:38427600-38443600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:38429200-38443800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:38430600-38444000	Weak transcription	HSMM	muscle
16	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
17	chr19:38432800-38443800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:38433000-38444000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:38434000-38447800	Weak transcription	Hela-S3	cervix
20	chr19:38434400-38444200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:38434400-38451800	Weak transcription	Primary T cells from cord blood	blood
22	chr19:38435200-38444000	Weak transcription	Colonic Mucosa	Colon
23	chr19:38436600-38443800	Weak transcription	Fetal Intestine Large	intestine
24	chr19:38436600-38444000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:38438400-38455600	Enhancers	Primary B cells from peripheral blood	blood
26	chr19:38439000-38445200	Weak transcription	Fetal Heart	heart
27	chr19:38439600-38443800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr19:38439600-38453000	Weak transcription	Gastric	stomach
29	chr19:38440000-38444200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr19:38440000-38446400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:38440800-38449600	Enhancers	Primary B cells from cord blood	blood
32	chr19:38441000-38445200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr19:38441000-38446600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:38441600-38443600	Weak transcription	NH-A	brain
36	chr19:38441600-38443800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:38441600-38445200	Enhancers	Osteobl	bone
38	chr19:38441600-38449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:38441800-38443600	Weak transcription	Psoas Muscle	Psoas
40	chr19:38441800-38443800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:38441800-38445600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr19:38442000-38445000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr19:38442000-38445600	Enhancers	GM12878-XiMat	blood
44	chr19:38442000-38445800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:38442200-38445000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr19:38442400-38445200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:38442400-38445400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr19:38442600-38444400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:38442600-38444600	Enhancers	HMEC	breast
50	chr19:38442600-38445200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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