Variant report

Variant	rs12460539
Chromosome Location	chr19:44936883-44936884
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44934142..44937093-chr6:166254130..166255662,2	MCF-7	breast:
2	chr19:44931433..44933674-chr19:44935471..44937509,2	K562	blood:
3	chr19:44932216..44933778-chr19:44935937..44937487,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16979070	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204543	0.95[ASN][1000 genomes]
rs204547	0.99[ASN][1000 genomes]
rs2571171	0.95[ASN][1000 genomes]
rs57014690	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59505617	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7246659	0.96[ASN][1000 genomes]
rs8101705	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113370	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1062330	chr19:44863939-44938277	Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv2763206	chr19:44885379-44941728	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3318557	chr19:44892181-44938875	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3318558	chr19:44892356-44938748	Active TSS ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv9734	chr19:44892761-44940023	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2756827	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2758764	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1059267	chr19:44896386-44938277	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1055870	chr19:44896386-44938779	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv2421963	chr19:44896398-44938791	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv442465	chr19:44896398-44938791	ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription 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	2 gene(s)	inside rSNPs	diseases
15	nsv1058295	chr19:44896888-44938779	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1065703	chr19:44898759-44938779	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1065424	chr19:44899546-44938779	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv16323	chr19:44928244-44938721	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44928000-44943600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr19:44928200-44941000	ZNF genes & repeats	Liver	Liver
3	chr19:44928200-44941000	ZNF genes & repeats	Ovary	ovary
4	chr19:44928200-44943400	ZNF genes & repeats	Adipose Nuclei	Adipose
5	chr19:44928400-44951800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:44929200-44945400	ZNF genes & repeats	Brain Germinal Matrix	brain
7	chr19:44929400-44941000	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:44931800-44940200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:44931800-44941000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
10	chr19:44931800-44941600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:44932000-44938800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:44932000-44939800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr19:44932000-44940000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:44932000-44941000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr19:44932000-44943400	ZNF genes & repeats	Fetal Lung	lung
16	chr19:44932000-44953200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr19:44932200-44937400	ZNF genes & repeats	Fetal Brain Male	brain
18	chr19:44932200-44937800	ZNF genes & repeats	HSMMtube	muscle
19	chr19:44932200-44940200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:44932200-44940400	ZNF genes & repeats	Brain Hippocampus Middle	brain
21	chr19:44932200-44940800	ZNF genes & repeats	Colon Smooth Muscle	Colon
22	chr19:44932200-44941000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:44932200-44941000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr19:44932200-44941000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:44932200-44941000	ZNF genes & repeats	Left Ventricle	heart
26	chr19:44932200-44943400	ZNF genes & repeats	A549	lung
27	chr19:44932200-44943600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
28	chr19:44932400-44937600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:44932400-44940200	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr19:44932400-44940800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
31	chr19:44932400-44940800	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr19:44932400-44941000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:44932400-44941000	ZNF genes & repeats	Aorta	Aorta
34	chr19:44932400-44941000	ZNF genes & repeats	Fetal Stomach	stomach
35	chr19:44932600-44941000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:44932600-44941000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:44932600-44941000	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr19:44932800-44937000	Strong transcription	Right Ventricle	heart
39	chr19:44932800-44940800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:44933800-44941200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:44934400-44938400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:44934600-44937800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:44934600-44937800	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:44934600-44950800	Weak transcription	Hela-S3	cervix
45	chr19:44934800-44938200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:44935200-44941000	ZNF genes & repeats	Brain Anterior Caudate	brain
47	chr19:44935600-44940800	ZNF genes & repeats	Spleen	Spleen
48	chr19:44935800-44937800	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr19:44935800-44942200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
50	chr19:44936000-44951400	Weak transcription	Fetal Heart	heart

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