Variant report

Variant	rs59459325
Chromosome Location	chr19:41175390-41175391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41167496..41181822-chr19:41192475..41200102,20	MCF-7	breast:
2	chr19:41167833..41170600-chr19:41173317..41176394,3	MCF-7	breast:
3	chr19:41171985..41176323-chr19:41183438..41185742,3	MCF-7	breast:
4	chr19:41173473..41175740-chr19:41257200..41259072,2	MCF-7	breast:
5	chr19:41173668..41175905-chr19:41178921..41181635,2	K562	blood:

Variant related genes	Relation type
ENSG00000077312	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000105245	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10401344	0.87[ASN][1000 genomes]
rs10404911	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426415	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288450	0.82[EUR][1000 genomes]
rs28493229	0.81[EUR][1000 genomes]
rs3815912	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45545932	0.94[ASN][1000 genomes]
rs73546894	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73931344	0.93[AFR][1000 genomes]
rs73931345	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8109754	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv2489	chr19:41145034-41182170	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 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	chr19:41169800-41184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr19:41169800-41195400	Weak transcription	Psoas Muscle	Psoas
3	chr19:41170000-41175400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:41170000-41178400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:41170000-41180400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:41170000-41180400	Weak transcription	Right Atrium	heart
7	chr19:41170000-41180800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:41172000-41193000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:41172200-41175600	Strong transcription	Fetal Stomach	stomach
10	chr19:41172400-41191000	Strong transcription	Stomach Smooth Muscle	stomach
11	chr19:41172600-41175400	Strong transcription	Lung	lung
12	chr19:41172600-41176200	Strong transcription	NHLF	lung
13	chr19:41172600-41193400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:41172600-41193600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:41172800-41175400	Strong transcription	Brain Hippocampus Middle	brain
16	chr19:41172800-41180000	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:41172800-41180200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:41172800-41180600	Strong transcription	Liver	Liver
19	chr19:41172800-41180800	Strong transcription	Colonic Mucosa	Colon
20	chr19:41172800-41191000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr19:41172800-41192000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr19:41172800-41192800	Strong transcription	Adipose Nuclei	Adipose
23	chr19:41172800-41193200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:41172800-41193200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:41173000-41175400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:41173000-41177000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:41173000-41179200	Strong transcription	Right Ventricle	heart
28	chr19:41173000-41183000	Weak transcription	Stomach Mucosa	stomach
29	chr19:41173000-41184000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr19:41173000-41185200	Strong transcription	Aorta	Aorta
31	chr19:41173000-41192800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:41173000-41192800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:41173000-41192800	Strong transcription	Ovary	ovary
34	chr19:41173000-41193200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:41173000-41193200	Strong transcription	Osteobl	bone
36	chr19:41173200-41175400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:41173200-41177000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:41173200-41180400	Strong transcription	Gastric	stomach
39	chr19:41173200-41180600	Strong transcription	Esophagus	oesophagus
40	chr19:41173200-41180800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr19:41173200-41187200	Strong transcription	Fetal Intestine Large	intestine
42	chr19:41173200-41189800	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr19:41173200-41192600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr19:41173200-41192800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:41173200-41193200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:41173400-41175400	Strong transcription	HUVEC	blood vessel
47	chr19:41173400-41180600	Strong transcription	Pancreas	Pancrea
48	chr19:41173600-41176800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr19:41173600-41180600	Strong transcription	Placenta	Placenta
50	chr19:41173600-41180800	Strong transcription	Duodenum Mucosa	Duodenum

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