Variant report

Variant	rs1055654
Chromosome Location	chr1:94007922-94007923
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10874786	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10874790	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11164936	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11164938	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11164942	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164943	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12042552	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12123339	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12135266	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12742850	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1812668	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs237438	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs237439	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2624436	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2624439	0.93[EUR][1000 genomes]
rs3767967	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847245	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4847428	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4847429	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4847431	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7546702	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7551016	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8179368	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[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	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
2	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1055654	TMED5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93964600-94015200	Weak transcription	Fetal Brain Male	brain
2	chr1:93965000-94013200	Weak transcription	Adipose Nuclei	Adipose
3	chr1:93965000-94017400	Weak transcription	Stomach Mucosa	stomach
4	chr1:93973200-94016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:93973400-94032000	Weak transcription	Esophagus	oesophagus
6	chr1:93984200-94017400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:93984800-94016000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:93985200-94012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:93985600-94012000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:93985600-94014200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:93985600-94014200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:93985600-94017600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:93985800-94015200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:93985800-94017800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:93986000-94013600	Weak transcription	Hela-S3	cervix
16	chr1:93986000-94017600	Weak transcription	NHEK	skin
17	chr1:93987000-94015200	Weak transcription	Ovary	ovary
18	chr1:93989000-94012200	Weak transcription	Dnd41	blood
19	chr1:93990000-94009800	Weak transcription	Fetal Kidney	kidney
20	chr1:93992000-94014200	Weak transcription	Pancreas	Pancrea
21	chr1:93992000-94018000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:93992200-94013000	Weak transcription	HMEC	breast
23	chr1:93992200-94013800	Weak transcription	Left Ventricle	heart
24	chr1:93992200-94017800	Weak transcription	Gastric	stomach
25	chr1:93992200-94018400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:93993400-94014200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:93994000-94012800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:93994200-94013200	Weak transcription	Placenta	Placenta
29	chr1:93995000-94045000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:93995600-94018000	Weak transcription	Primary T cells from cord blood	blood
31	chr1:93997200-94013600	Weak transcription	NH-A	brain
32	chr1:93997400-94010200	Weak transcription	HSMM	muscle
33	chr1:93997400-94017600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:93997600-94011800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:93997600-94013000	Weak transcription	Brain Germinal Matrix	brain
36	chr1:93997600-94013000	Weak transcription	HepG2	liver
37	chr1:93997600-94018200	Weak transcription	A549	lung
38	chr1:93997800-94008200	Weak transcription	Fetal Intestine Large	intestine
39	chr1:93997800-94010800	Weak transcription	Fetal Intestine Small	intestine
40	chr1:93997800-94012400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:93997800-94012800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:93997800-94013400	Weak transcription	Primary B cells from cord blood	blood
43	chr1:93997800-94014200	Weak transcription	Fetal Stomach	stomach
44	chr1:93997800-94015200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:93997800-94015200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:93998000-94011800	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:93998000-94014200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:93998400-94014400	Weak transcription	Fetal Brain Female	brain
49	chr1:93998600-94010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:93999000-94012400	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links