Variant report

Variant	rs1643465
Chromosome Location	chr19:38461440-38461441
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38459331..38461760-chr19:38470604..38472306,2	MCF-7	breast:
2	chr19:38421858..38424190-chr19:38460757..38462357,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1632177	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643470	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643472	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725468	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1725486	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1725490	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs353405	0.81[EUR][1000 genomes]
rs353406	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs353409	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs353412	0.83[EUR][1000 genomes]
rs353413	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803566	0.80[EUR][1000 genomes]
rs697433	0.81[EUR][1000 genomes]
rs8102871	0.80[EUR][1000 genomes]
rs8110417	0.81[EUR][1000 genomes]
rs8111400	0.81[EUR][1000 genomes]
rs833915	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs833916	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs861308	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38457200-38470400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:38457600-38470200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:38457600-38470400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:38457600-38470400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr19:38457800-38468200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:38457800-38468400	Weak transcription	NH-A	brain
7	chr19:38458200-38468600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:38459000-38464800	ZNF genes & repeats	A549	lung
9	chr19:38459200-38463400	ZNF genes & repeats	GM12878-XiMat	blood
10	chr19:38459400-38463800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:38460200-38461600	ZNF genes & repeats	Primary T cells from cord blood	blood
12	chr19:38460200-38463800	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr19:38460400-38461800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr19:38460400-38462200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
15	chr19:38460400-38463800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:38460600-38468200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:38460800-38461600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr19:38460800-38461600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
19	chr19:38460800-38461800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr19:38460800-38462200	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr19:38460800-38462200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr19:38461000-38461600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:38461000-38461600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:38461000-38461600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:38461000-38461600	ZNF genes & repeats	Left Ventricle	heart
26	chr19:38461000-38461600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
27	chr19:38461000-38461600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
28	chr19:38461000-38461600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
29	chr19:38461000-38461600	ZNF genes & repeats	Spleen	Spleen
30	chr19:38461000-38461600	ZNF genes & repeats	Osteobl	bone
31	chr19:38461000-38461800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
32	chr19:38461000-38461800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:38461000-38461800	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr19:38461000-38462000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:38461000-38462000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:38461000-38462000	ZNF genes & repeats	Aorta	Aorta
37	chr19:38461000-38462000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
38	chr19:38461000-38462600	ZNF genes & repeats	Fetal Stomach	stomach
39	chr19:38461000-38463800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr19:38461000-38468200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:38461200-38461600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:38461200-38461600	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:38461200-38461600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:38461200-38461600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
45	chr19:38461200-38461600	ZNF genes & repeats	Gastric	stomach
46	chr19:38461200-38461600	ZNF genes & repeats	Lung	lung
47	chr19:38461200-38461600	ZNF genes & repeats	HSMM	muscle
48	chr19:38461200-38461600	ZNF genes & repeats	NHDF-Ad	bronchial
49	chr19:38461200-38461800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:38461200-38461800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle

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