Variant report

Variant	rs10874790
Chromosome Location	chr1:93971502-93971503
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93963303..93967401-chr1:93968179..93972318,5	K562	blood:
2	chr1:93645495..93647444-chr1:93968809..93971761,2	K562	blood:

Variant related genes	Relation type
ENSG00000122483	Chromatin interaction
ENSG00000117500	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1055654	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10874786	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164924	0.88[ASN][1000 genomes]
rs11164936	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11164938	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164942	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164943	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12042552	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12123339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12135266	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12742850	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812668	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs237438	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs237439	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2391271	0.89[ASN][1000 genomes]
rs2624436	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2624439	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35102250	0.85[ASN][1000 genomes]
rs3767967	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847428	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4847429	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847431	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7546702	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7551016	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8179368	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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	nsv1011853	chr1:93966450-94039005	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10874790	RP4-717I23.3	cis	Artery Tibial	GTEx
rs10874790	TMED5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93943200-93974400	Weak transcription	Fetal Lung	lung
2	chr1:93944000-93974600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:93944200-93971800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:93944200-93974800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:93946800-93973200	Weak transcription	Fetal Intestine Small	intestine
6	chr1:93950400-93974800	Weak transcription	HepG2	liver
7	chr1:93951000-93972800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:93952600-93973600	Weak transcription	Brain Germinal Matrix	brain
9	chr1:93956200-93974000	Weak transcription	HMEC	breast
10	chr1:93956400-93975200	Weak transcription	Fetal Stomach	stomach
11	chr1:93958000-93997200	Weak transcription	HSMMtube	muscle
12	chr1:93958800-93991800	Weak transcription	Gastric	stomach
13	chr1:93959000-93974800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:93960200-93974400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:93961000-93988400	Weak transcription	HUVEC	blood vessel
16	chr1:93962600-93984200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:93964000-93972800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:93964400-93974800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:93964600-93973000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:93964600-93990200	Weak transcription	HSMM	muscle
21	chr1:93964600-94015200	Weak transcription	Fetal Brain Male	brain
22	chr1:93964800-93974400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:93964800-93974600	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:93965000-94013200	Weak transcription	Adipose Nuclei	Adipose
25	chr1:93965000-94017400	Weak transcription	Stomach Mucosa	stomach
26	chr1:93965200-93974200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:93965200-93974600	Weak transcription	Fetal Kidney	kidney
28	chr1:93965200-93974800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:93965200-93984600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:93965200-93984800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:93965400-93983600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:93965800-93974400	Weak transcription	Fetal Brain Female	brain
33	chr1:93965800-93974800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:93965800-93974800	Weak transcription	Primary T cells from cord blood	blood
35	chr1:93966000-93975200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:93966400-93972400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:93966400-93974400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:93967000-93974400	Weak transcription	Dnd41	blood
39	chr1:93967200-93971800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:93967200-93974400	Weak transcription	Fetal Intestine Large	intestine
41	chr1:93967400-93973800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:93967400-93984200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:93968600-93972800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:93968600-93973000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:93968600-93974000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:93968600-93976800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:93968600-93984400	Weak transcription	NHEK	skin
48	chr1:93968800-93972800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:93969000-93974200	Weak transcription	Right Atrium	heart
50	chr1:93970000-93971800	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links