Variant report

Variant	rs25478
Chromosome Location	chr19:44049861-44049862
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44048400..44050910-chr19:44143121..44145462,2	MCF-7	breast:
2	chr19:44046417..44049052-chr19:44049423..44052069,2	MCF-7	breast:
3	chr19:44049826..44052731-chr19:44057585..44060177,2	MCF-7	breast:
4	chr19:44048671..44051065-chr19:44122727..44124528,2	K562	blood:

Variant related genes	Relation type
ENSG00000269177	Chromatin interaction
ENSG00000131116	Chromatin interaction
ENSG00000105767	Chromatin interaction
ENSG00000073050	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17725124	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1799782	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2293036	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3213277	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3213344	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3213376	1.00[EUR][1000 genomes]
rs3213403	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][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	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv912107	chr19:44030998-44055726	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	esv3449530	chr19:44049707-44049909	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44038600-44054000	Weak transcription	Psoas Muscle	Psoas
2	chr19:44038800-44055800	Weak transcription	Stomach Mucosa	stomach
3	chr19:44039200-44078600	Weak transcription	Hela-S3	cervix
4	chr19:44040200-44052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:44040200-44052200	Strong transcription	Fetal Muscle Leg	muscle
6	chr19:44040600-44050000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:44040600-44052000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:44040800-44051800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr19:44040800-44060800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:44041400-44050200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:44041400-44050200	Strong transcription	Primary T cells from cord blood	blood
12	chr19:44041400-44050600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:44041600-44050000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr19:44041600-44051200	Strong transcription	Spleen	Spleen
15	chr19:44041600-44051400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr19:44041600-44051600	Strong transcription	Fetal Intestine Large	intestine
17	chr19:44041600-44052200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:44041800-44050400	Strong transcription	Ovary	ovary
19	chr19:44041800-44065200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:44042000-44051600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:44042000-44051600	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr19:44042200-44050400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:44042200-44050400	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr19:44042400-44050000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:44042400-44050200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:44042400-44050200	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:44042400-44050200	Strong transcription	HSMM	muscle
28	chr19:44042400-44050400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr19:44042400-44051200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:44042400-44052000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr19:44042400-44058000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr19:44042600-44050000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:44042600-44052000	Strong transcription	Placenta	Placenta
34	chr19:44043200-44050200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:44043200-44051800	Strong transcription	Brain Hippocampus Middle	brain
36	chr19:44043200-44064600	Weak transcription	NHDF-Ad	bronchial
37	chr19:44043400-44051400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr19:44043400-44051400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:44043400-44051600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:44043400-44052200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:44043400-44058800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:44043400-44059000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr19:44043400-44059200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:44043600-44050000	Strong transcription	Brain Cingulate Gyrus	brain
45	chr19:44043600-44050000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr19:44043600-44051600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr19:44043600-44052000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:44043600-44054600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr19:44043600-44057800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr19:44043600-44059200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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