Variant report

Variant	rs16975859
Chromosome Location	chr19:38311843-38311844
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38310273..38312700-chr19:38313306..38315862,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L3-3	chr19:38310864-38314365	NONHSAT066169

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs16958869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16972326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16974061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16974358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16975375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16975696	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16975712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16975753	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2061779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2290998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2306200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3745940	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3745941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3795068	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3795070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41325249	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4330033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73633159	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic 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 miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38308600-38312000	Weak transcription	Aorta	Aorta
2	chr19:38308600-38314800	Weak transcription	Gastric	stomach
3	chr19:38308800-38312000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:38308800-38312000	Weak transcription	Fetal Intestine Large	intestine
5	chr19:38308800-38312200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr19:38308800-38312200	Weak transcription	Left Ventricle	heart
7	chr19:38308800-38313200	Weak transcription	Esophagus	oesophagus
8	chr19:38308800-38314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:38308800-38314400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:38308800-38314400	Weak transcription	Brain Angular Gyrus	brain
11	chr19:38308800-38314400	Weak transcription	Fetal Muscle Leg	muscle
12	chr19:38308800-38314400	Weak transcription	Right Ventricle	heart
13	chr19:38308800-38314600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:38308800-38314600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:38308800-38314600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr19:38308800-38315400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr19:38309000-38312000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:38309000-38313000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:38309000-38313200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:38309000-38314200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:38309000-38314200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:38309000-38314600	Weak transcription	Fetal Heart	heart
23	chr19:38309000-38316800	Weak transcription	Stomach Mucosa	stomach
24	chr19:38309400-38315000	Weak transcription	Placenta	Placenta
25	chr19:38309600-38314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:38309600-38319200	ZNF genes & repeats	Fetal Brain Female	brain
27	chr19:38310000-38312000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr19:38310000-38312400	Strong transcription	Brain Cingulate Gyrus	brain
29	chr19:38310000-38317000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr19:38310000-38317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:38310000-38318200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:38310200-38312000	Strong transcription	Pancreatic Islets	Pancreatic Islet
33	chr19:38310200-38312000	Strong transcription	Ovary	ovary
34	chr19:38310200-38312600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr19:38310200-38313800	ZNF genes & repeats	Fetal Brain Male	brain
36	chr19:38310200-38317600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
37	chr19:38310400-38312800	Strong transcription	Brain Hippocampus Middle	brain
38	chr19:38310600-38315000	Weak transcription	Pancreas	Pancrea
39	chr19:38310800-38312000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:38310800-38312400	Strong transcription	Brain Anterior Caudate	brain
41	chr19:38310800-38313600	ZNF genes & repeats	Adipose Nuclei	Adipose
42	chr19:38310800-38314000	Strong transcription	Fetal Lung	lung
43	chr19:38311000-38312000	Strong transcription	Brain Germinal Matrix	brain
44	chr19:38311000-38313800	Weak transcription	Brain Substantia Nigra	brain
45	chr19:38311000-38314400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr19:38311400-38312400	Strong transcription	Fetal Kidney	kidney
47	chr19:38311400-38314600	Weak transcription	Fetal Stomach	stomach
48	chr19:38311600-38312200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr19:38311600-38312400	ZNF genes & repeats	Colon Smooth Muscle	Colon
50	chr19:38311800-38312000	Strong transcription	Rectal Smooth Muscle	rectum

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