Variant report

Variant	rs1725506
Chromosome Location	chr19:38557237-38557238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPINT2-8	chr19:38556989-38557339	expReg_chr19_4921_+

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10405667	0.82[ASN][1000 genomes]
rs10413751	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1568975	0.80[ASN][1000 genomes]
rs1614979	0.80[ASN][1000 genomes]
rs1622409	0.84[ASN][1000 genomes]
rs1654347	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1654349	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654350	0.85[EUR][1000 genomes]
rs1654352	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654355	0.80[ASN][1000 genomes]
rs1654357	0.80[ASN][1000 genomes]
rs1654359	0.80[ASN][1000 genomes]
rs1725458	0.81[EUR][1000 genomes]
rs1725461	0.84[ASN][1000 genomes]
rs1725462	0.81[EUR][1000 genomes]
rs1725470	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1725475	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1725476	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1725479	0.80[ASN][1000 genomes]
rs1725507	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1725508	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1725509	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1725510	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28587798	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4802233	0.80[ASN][1000 genomes]
rs57585457	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57999412	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58152231	0.80[ASN][1000 genomes]
rs705505	0.80[ASN][1000 genomes]
rs7257303	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729625	0.84[ASN][1000 genomes]
rs735615	0.80[ASN][1000 genomes]
rs855597	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs855598	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs855599	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs855600	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs855601	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs855602	0.81[EUR][1000 genomes]
rs855603	0.83[AFR][1000 genomes]
rs855621	0.80[ASN][1000 genomes]
rs855623	0.84[ASN][1000 genomes]
rs855636	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs855637	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs855638	0.80[ASN][1000 genomes]
rs855640	0.80[ASN][1000 genomes]
rs941040	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
2	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
3	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
4	chr19:38543800-38563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr19:38547000-38563600	Weak transcription	Fetal Lung	lung
7	chr19:38547200-38561400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38549200-38564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:38549200-38572000	Weak transcription	Liver	Liver
10	chr19:38549400-38560000	Weak transcription	Psoas Muscle	Psoas
11	chr19:38549600-38572600	Weak transcription	Thymus	Thymus
12	chr19:38550000-38561000	Weak transcription	Hela-S3	cervix
13	chr19:38550000-38570400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr19:38550800-38563400	Weak transcription	Spleen	Spleen
15	chr19:38550800-38565200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr19:38550800-38570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:38550800-38572200	Weak transcription	Colonic Mucosa	Colon
18	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:38551000-38572000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:38551200-38562200	Weak transcription	Primary T cells from cord blood	blood
21	chr19:38551200-38562600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:38551200-38563600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr19:38551200-38567000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr19:38551400-38562400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:38551400-38567000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:38552400-38560800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:38552400-38561000	Weak transcription	NHEK	skin
29	chr19:38552400-38561200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:38552600-38559800	Weak transcription	HSMMtube	muscle
31	chr19:38552800-38560000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:38553000-38559400	Strong transcription	A549	lung
33	chr19:38553000-38559600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:38553000-38559800	Weak transcription	NHDF-Ad	bronchial
35	chr19:38553200-38570400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:38553600-38557800	Weak transcription	GM12878-XiMat	blood
37	chr19:38553800-38561200	Weak transcription	NH-A	brain
38	chr19:38553800-38561400	Weak transcription	Esophagus	oesophagus
39	chr19:38553800-38561400	Weak transcription	Lung	lung
40	chr19:38553800-38572000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:38554200-38561400	Weak transcription	Pancreas	Pancrea
42	chr19:38554200-38572600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:38554400-38559600	Weak transcription	Gastric	stomach
44	chr19:38554400-38560000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:38554400-38561000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr19:38554400-38564600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:38554600-38561000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:38554600-38567000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr19:38554600-38570400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:38554600-38571800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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