Variant report

Variant	rs73541344
Chromosome Location	chr19:19843047-19843048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19626852..19628495-chr19:19842334..19845203,2	MCF-7	breast:
2	chr19:19842192..19843794-chr19:19857515..19860071,2	K562	blood:
3	chr19:19772731..19775725-chr19:19841970..19845590,5	MCF-7	breast:
4	chr19:19772622..19775616-chr19:19842700..19844547,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258674	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000186010	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11878966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879251	1.00[EUR][1000 genomes]
rs11880104	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882164	1.00[EUR][1000 genomes]
rs11883102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996269	1.00[AMR][1000 genomes]
rs17378427	1.00[EUR][1000 genomes]
rs34087491	1.00[EUR][1000 genomes]
rs57474361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58294398	1.00[EUR][1000 genomes]
rs60101043	1.00[EUR][1000 genomes]
rs60133934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60610603	1.00[EUR][1000 genomes]
rs61489113	1.00[EUR][1000 genomes]
rs66969937	0.88[AFR][1000 genomes]
rs7247366	1.00[EUR][1000 genomes]
rs7248802	1.00[EUR][1000 genomes]
rs7250144	1.00[EUR][1000 genomes]
rs7253515	1.00[EUR][1000 genomes]
rs7257247	1.00[EUR][1000 genomes]
rs7258865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73537247	1.00[EUR][1000 genomes]
rs73537262	1.00[EUR][1000 genomes]
rs73537266	1.00[EUR][1000 genomes]
rs73539233	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73539261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73541334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73541360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73541377	1.00[EUR][1000 genomes]
rs8105557	1.00[EUR][1000 genomes]
rs8111841	1.00[EUR][1000 genomes]
rs8112744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8113100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9676945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1065704	chr19:19797999-19865818	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv543929	chr19:19797999-19865818	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1062017	chr19:19803482-19865818	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv543930	chr19:19803482-19865818	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1057601	chr19:19803482-19873623	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic 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	14 gene(s)	inside rSNPs	diseases
9	nsv1063535	chr19:19806386-19863631	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1062212	chr19:19806386-19869332	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1060122	chr19:19814678-19879575	Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv2436	chr19:19815858-19869171	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv911311	chr19:19831544-19863284	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19828400-19843200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:19840400-19843200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:19840400-19843200	Weak transcription	Gastric	stomach
4	chr19:19840600-19844400	ZNF genes & repeats	Liver	Liver
5	chr19:19842000-19844400	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr19:19842400-19843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:19842400-19843200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:19842400-19843200	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr19:19842400-19844200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
10	chr19:19842400-19844200	Active TSS	Hela-S3	cervix
11	chr19:19842400-19844400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:19842400-19844400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:19842400-19844400	Active TSS	GM12878-XiMat	blood
14	chr19:19842400-19844600	Active TSS	Stomach Smooth Muscle	stomach
15	chr19:19842400-19844800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr19:19842600-19843200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr19:19842600-19843200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:19842600-19843200	Enhancers	Pancreas	Pancrea
19	chr19:19842600-19843200	Enhancers	Spleen	Spleen
20	chr19:19842600-19843200	Flanking Active TSS	Dnd41	blood
21	chr19:19842600-19843400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr19:19842600-19843400	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
23	chr19:19842600-19843600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:19842600-19843600	Flanking Active TSS	Right Ventricle	heart
25	chr19:19842600-19843800	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr19:19842600-19844200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr19:19842600-19844200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:19842600-19844200	Active TSS	HSMM	muscle
29	chr19:19842600-19844400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr19:19842600-19844400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:19842600-19844400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:19842600-19844400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:19842600-19844400	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr19:19842600-19844400	Active TSS	Rectal Smooth Muscle	rectum
35	chr19:19842600-19844600	Active TSS	Placenta	Placenta
36	chr19:19842800-19843200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:19842800-19843200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr19:19842800-19843200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:19842800-19843200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr19:19842800-19843200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:19842800-19843200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr19:19842800-19843200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr19:19842800-19843200	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr19:19842800-19843200	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr19:19842800-19843200	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr19:19842800-19843200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr19:19842800-19843200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:19842800-19843200	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr19:19842800-19843200	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr19:19842800-19843200	Flanking Active TSS	Fetal Heart	heart

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