Variant report

Variant	rs57403354
Chromosome Location	chr19:39367312-39367313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39339114..39344809-chr19:39363672..39368217,5	MCF-7	breast:
2	chr19:39338470..39342492-chr19:39367140..39370147,4	K562	blood:
3	chr19:39361253..39362787-chr19:39366750..39368936,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RINL-1	chr19:39366971-39367421	NONHSAT066256

Variant related genes	Relation type
ENSG00000187994	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10405685	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13346505	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16972862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28391081	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45592833	0.84[AMR][1000 genomes]
rs58188607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73537642	1.00[EUR][1000 genomes]
rs73537687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39356200-39368000	Weak transcription	HepG2	liver
2	chr19:39360800-39371400	Weak transcription	NHLF	lung
3	chr19:39360800-39379200	Weak transcription	NHDF-Ad	bronchial
4	chr19:39361000-39370000	Weak transcription	Aorta	Aorta
5	chr19:39361000-39379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:39361000-39380200	Weak transcription	Psoas Muscle	Psoas
7	chr19:39361200-39367800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:39361200-39368200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr19:39361200-39368400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:39361200-39368400	Weak transcription	Stomach Mucosa	stomach
11	chr19:39361200-39368400	Weak transcription	HMEC	breast
12	chr19:39361200-39368600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:39361200-39368600	Weak transcription	Gastric	stomach
14	chr19:39361200-39368600	Weak transcription	Right Atrium	heart
15	chr19:39361200-39369200	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:39361200-39369400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:39361200-39369400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:39361200-39369600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:39361200-39369800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:39361200-39369800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:39361200-39369800	Weak transcription	Pancreas	Pancrea
22	chr19:39361200-39370000	Weak transcription	Brain Substantia Nigra	brain
23	chr19:39361200-39370400	Weak transcription	Brain Angular Gyrus	brain
24	chr19:39361200-39370600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:39361200-39370800	Weak transcription	Ovary	ovary
26	chr19:39361200-39371000	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:39361200-39371200	Weak transcription	Liver	Liver
28	chr19:39361200-39376800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:39361400-39367800	Weak transcription	GM12878-XiMat	blood
30	chr19:39361400-39368000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr19:39361400-39368200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr19:39361400-39368200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:39361400-39368200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr19:39361400-39368400	Weak transcription	Fetal Thymus	thymus
35	chr19:39361400-39368400	Weak transcription	Left Ventricle	heart
36	chr19:39361400-39368400	Weak transcription	Lung	lung
37	chr19:39361400-39368400	Weak transcription	Thymus	Thymus
38	chr19:39361400-39368600	Weak transcription	Esophagus	oesophagus
39	chr19:39361400-39368600	Weak transcription	Fetal Stomach	stomach
40	chr19:39361400-39369200	Weak transcription	Brain Germinal Matrix	brain
41	chr19:39361400-39369200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr19:39361600-39368000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:39361600-39368000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:39361600-39368000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:39361600-39368200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr19:39361600-39368200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr19:39361600-39368600	Weak transcription	Placenta	Placenta
48	chr19:39361600-39369200	Weak transcription	Right Ventricle	heart
49	chr19:39361600-39369800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:39361800-39367400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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