Variant report

Variant	rs28510490
Chromosome Location	chr15:83705796-83705797
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	chr15:83681301..83683584-chr15:83704443..83706244,2	K562	blood:
2	chr15:83680792..83683584-chr15:83704302..83706244,2	K562	blood:

Variant related genes	Relation type
ENSG00000260608	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10220725	1.00[ASN][1000 genomes]
rs17295457	1.00[ASN][1000 genomes]
rs28408839	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429062	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454771	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463621	1.00[ASN][1000 genomes]
rs28479338	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28509292	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540116	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569354	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570610	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28662361	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28707195	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28711332	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28819476	1.00[ASN][1000 genomes]
rs28836869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67634629	1.00[ASN][1000 genomes]
rs7169539	1.00[ASN][1000 genomes]
rs7170046	1.00[ASN][1000 genomes]
rs72755930	1.00[ASN][1000 genomes]
rs72755935	1.00[ASN][1000 genomes]
rs72755947	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755962	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025896	0.97[AFR][1000 genomes]
rs8038619	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919979	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[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	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28510490	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681200-83710200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
3	chr15:83682000-83708400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:83682200-83708600	Weak transcription	Fetal Heart	heart
5	chr15:83683000-83723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:83687000-83708200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:83687600-83709600	Weak transcription	Brain Angular Gyrus	brain
9	chr15:83688800-83708800	Weak transcription	Fetal Brain Male	brain
10	chr15:83689400-83708600	Weak transcription	NHEK	skin
11	chr15:83690000-83708200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:83690000-83708800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:83690400-83708000	Weak transcription	Brain Germinal Matrix	brain
14	chr15:83695400-83714600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:83695800-83715400	Weak transcription	HSMMtube	muscle
16	chr15:83696400-83708200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:83697800-83721000	Strong transcription	Fetal Intestine Large	intestine
18	chr15:83698400-83708600	Weak transcription	Brain Anterior Caudate	brain
19	chr15:83698600-83708200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:83698600-83709600	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:83698800-83708200	Weak transcription	HUVEC	blood vessel
22	chr15:83698800-83708600	Weak transcription	HMEC	breast
23	chr15:83698800-83712000	Weak transcription	Colonic Mucosa	Colon
24	chr15:83699000-83707400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:83699000-83708200	Weak transcription	Left Ventricle	heart
26	chr15:83699000-83708200	Weak transcription	Ovary	ovary
27	chr15:83699000-83708200	Weak transcription	Right Ventricle	heart
28	chr15:83699000-83708200	Weak transcription	Spleen	Spleen
29	chr15:83699000-83708200	Weak transcription	NHLF	lung
30	chr15:83699000-83708400	Weak transcription	Pancreas	Pancrea
31	chr15:83699000-83708600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:83699000-83708600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:83699000-83708600	Weak transcription	Placenta	Placenta
34	chr15:83699000-83708800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:83699000-83709000	Weak transcription	Small Intestine	intestine
36	chr15:83699000-83710000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:83699000-83712000	Weak transcription	Gastric	stomach
38	chr15:83699000-83715800	Weak transcription	Brain Substantia Nigra	brain
39	chr15:83699000-83716800	Weak transcription	Aorta	Aorta
40	chr15:83699000-83725800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:83699200-83706200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:83699200-83708000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:83699200-83708000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:83699200-83708000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:83699200-83708600	Weak transcription	Osteobl	bone
46	chr15:83699200-83708800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr15:83699400-83708200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:83699400-83708800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr15:83699400-83708800	Weak transcription	NH-A	brain
50	chr15:83699600-83707400	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links