Variant report

Variant	rs1625884
Chromosome Location	chr19:38593982-38593983
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38396839..38398379-chr19:38593196..38595560,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10403716	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10405667	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10412865	0.82[EUR][1000 genomes]
rs10422665	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1568975	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1614979	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1622409	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1654355	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1654357	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1654358	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654359	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1654365	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1654367	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1725461	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1725473	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1725479	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1725512	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2005054	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2082442	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2082443	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28412601	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28581256	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28587798	0.86[ASN][1000 genomes]
rs3760882	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810356	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802233	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802239	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4802247	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4803786	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803800	0.87[EUR][1000 genomes]
rs4803801	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803802	0.87[EUR][1000 genomes]
rs4803803	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803809	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803810	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56166457	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56293547	0.87[EUR][1000 genomes]
rs58152231	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59185302	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59579475	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59924887	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61388128	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs705505	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71179415	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7248428	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7250034	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs729625	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs729626	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs735615	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs754123	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8105468	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8106266	0.86[EUR][1000 genomes]
rs855597	0.84[ASN][1000 genomes]
rs855600	0.88[ASN][1000 genomes]
rs855601	0.88[ASN][1000 genomes]
rs855602	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs855603	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs855619	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs855621	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs855623	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs855624	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs855625	0.88[EUR][1000 genomes]
rs855627	0.91[EUR][1000 genomes]
rs855630	0.95[EUR][1000 genomes]
rs855631	0.84[EUR][1000 genomes]
rs855633	0.92[EUR][1000 genomes]
rs855634	0.92[EUR][1000 genomes]
rs855638	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs855640	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs855641	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs860623	0.90[EUR][1000 genomes]
rs863020	0.91[EUR][1000 genomes]
rs941039	0.92[EUR][1000 genomes]
rs941040	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9941456	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9941467	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1625884	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:38573600-38610000	Strong transcription	Fetal Intestine Large	intestine
4	chr19:38580400-38594800	Weak transcription	HSMMtube	muscle
5	chr19:38580600-38596000	Weak transcription	Stomach Mucosa	stomach
6	chr19:38581600-38610000	Weak transcription	Psoas Muscle	Psoas
7	chr19:38584400-38597000	Weak transcription	Right Atrium	heart
8	chr19:38584800-38602400	Weak transcription	Fetal Brain Male	brain
9	chr19:38584800-38602400	Weak transcription	Fetal Heart	heart
10	chr19:38587000-38605400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr19:38587200-38603200	Strong transcription	Primary B cells from cord blood	blood
12	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr19:38588600-38597200	Strong transcription	Osteobl	bone
15	chr19:38588600-38604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:38588800-38606600	Strong transcription	Liver	Liver
17	chr19:38589200-38606800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr19:38589400-38595200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:38590000-38594000	Strong transcription	Rectal Smooth Muscle	rectum
20	chr19:38590200-38594000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:38590200-38597200	Strong transcription	Gastric	stomach
22	chr19:38590200-38605200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:38590200-38605800	Strong transcription	Adipose Nuclei	Adipose
24	chr19:38590200-38606600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:38590200-38606600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr19:38590200-38611000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr19:38590400-38594000	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:38590400-38595000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr19:38590400-38599200	Strong transcription	Pancreas	Pancrea
30	chr19:38590400-38606400	Strong transcription	Fetal Brain Female	brain
31	chr19:38590400-38609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr19:38590800-38594000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr19:38590800-38594000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr19:38590800-38596800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:38590800-38597200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:38590800-38602800	Strong transcription	Spleen	Spleen
37	chr19:38590800-38603600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr19:38590800-38603800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr19:38590800-38606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:38590800-38608800	Strong transcription	Fetal Intestine Small	intestine
41	chr19:38591000-38595200	Strong transcription	Fetal Muscle Leg	muscle
42	chr19:38591000-38596200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:38591000-38596200	Weak transcription	Hela-S3	cervix
44	chr19:38591000-38601800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:38591000-38605000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:38591200-38594000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:38591200-38596200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr19:38591200-38597000	Weak transcription	HUVEC	blood vessel
49	chr19:38591200-38597200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:38591200-38597200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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