Variant report

Variant	rs45601936
Chromosome Location	chr19:39840619-39840620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39840535..39845164-chr19:39896257..39899085,6	K562	blood:
2	chr19:39830889..39835466-chr19:39836647..39841099,6	MCF-7	breast:
3	chr19:39838097..39840751-chr19:39908169..39910742,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MED29-3	chr19:39840440-39843129	NONHSAT066282

Variant related genes	Relation type
ENSG00000090924	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000179134	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs28370340	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30453	0.81[ASN][1000 genomes]
rs30454	0.81[ASN][1000 genomes]
rs30455	0.81[ASN][1000 genomes]
rs30456	0.81[ASN][1000 genomes]
rs30457	0.81[ASN][1000 genomes]
rs30458	0.81[ASN][1000 genomes]
rs36264	0.81[ASN][1000 genomes]
rs40353	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40441	0.81[ASN][1000 genomes]
rs562638	0.81[ASN][1000 genomes]
rs57310698	0.90[EUR][1000 genomes]
rs7246750	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250420	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102194	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
4	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
5	nsv911681	chr19:39797716-39856246	Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834000-39842400	Weak transcription	Gastric	stomach
2	chr19:39834200-39846600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:39834400-39841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:39834400-39841800	Weak transcription	Lung	lung
6	chr19:39834400-39842000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr19:39834400-39842000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:39834400-39842000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:39834400-39842200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:39834400-39842200	Weak transcription	Esophagus	oesophagus
11	chr19:39834400-39842400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr19:39834400-39844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:39834400-39845400	Weak transcription	Fetal Kidney	kidney
14	chr19:39834400-39849200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:39834600-39842400	Weak transcription	Colonic Mucosa	Colon
16	chr19:39834600-39842400	Weak transcription	HMEC	breast
17	chr19:39834800-39842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:39834800-39847400	Weak transcription	Small Intestine	intestine
19	chr19:39834800-39852800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:39834800-39852800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:39835000-39844600	Weak transcription	Stomach Mucosa	stomach
23	chr19:39835000-39846000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:39835600-39853600	Strong transcription	Placenta	Placenta
25	chr19:39835800-39841200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr19:39836000-39847600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr19:39836200-39842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:39836200-39842800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
32	chr19:39836400-39862600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr19:39836600-39845600	Weak transcription	Aorta	Aorta
34	chr19:39836600-39845800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:39836600-39864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
38	chr19:39836800-39842200	Weak transcription	Colon Smooth Muscle	Colon
39	chr19:39836800-39846000	Weak transcription	Pancreas	Pancrea
40	chr19:39836800-39852000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:39836800-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:39837000-39841200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr19:39837000-39841800	Strong transcription	Fetal Muscle Leg	muscle
44	chr19:39837000-39841800	Weak transcription	Psoas Muscle	Psoas
45	chr19:39837200-39842200	Strong transcription	Stomach Smooth Muscle	stomach
46	chr19:39837200-39842600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:39837400-39842400	Enhancers	Brain Cingulate Gyrus	brain
48	chr19:39837400-39842400	Weak transcription	Fetal Brain Male	brain
49	chr19:39837400-39846400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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