Variant report

Variant	rs1168404
Chromosome Location	chr5:68706825-68706826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10035835	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10038816	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10064264	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10068576	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10077458	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10078100	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168409	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168410	0.82[ASN][1000 genomes]
rs1177556	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1183278	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2561172	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2561186	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28703034	0.82[ASN][1000 genomes]
rs299075	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs299077	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299088	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs299091	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299094	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs299098	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299099	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs299102	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4252228	0.88[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	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1168404	CCDC125	cis	lung	GTEx
rs1168404	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs1168404	MRPS36	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68666600-68710800	Weak transcription	Esophagus	oesophagus
2	chr5:68666800-68710600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:68666800-68710600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:68666800-68710800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:68666800-68710800	Weak transcription	Psoas Muscle	Psoas
6	chr5:68667200-68710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:68667200-68710800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:68667800-68710600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:68668000-68713000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:68668800-68712400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:68675600-68708400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr5:68678600-68710200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:68685400-68710000	Weak transcription	Hela-S3	cervix
14	chr5:68688800-68710600	Weak transcription	Colonic Mucosa	Colon
15	chr5:68690000-68710600	Weak transcription	Right Ventricle	heart
16	chr5:68690200-68710600	Weak transcription	NHLF	lung
17	chr5:68690200-68710800	Weak transcription	Gastric	stomach
18	chr5:68690800-68707400	Weak transcription	HSMMtube	muscle
19	chr5:68690800-68710400	Weak transcription	HepG2	liver
20	chr5:68690800-68711200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:68691600-68710800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:68692200-68710600	Weak transcription	NH-A	brain
23	chr5:68692400-68708200	Weak transcription	HSMM	muscle
24	chr5:68692400-68710400	Weak transcription	Brain Substantia Nigra	brain
25	chr5:68692400-68710400	Weak transcription	Fetal Heart	heart
26	chr5:68693600-68710600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:68693600-68710600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:68694400-68707400	Weak transcription	Osteobl	bone
29	chr5:68695200-68708600	Weak transcription	Fetal Brain Male	brain
30	chr5:68696800-68710800	Weak transcription	Aorta	Aorta
31	chr5:68696800-68711000	Weak transcription	Small Intestine	intestine
32	chr5:68697000-68710400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:68697000-68710800	Weak transcription	Pancreas	Pancrea
34	chr5:68697200-68710600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:68697400-68707000	Weak transcription	HMEC	breast
36	chr5:68697400-68710600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr5:68697600-68707000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr5:68697600-68710200	Weak transcription	Fetal Kidney	kidney
39	chr5:68697600-68710600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:68697600-68710600	Weak transcription	Brain Anterior Caudate	brain
41	chr5:68697600-68710600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:68697800-68717000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:68698800-68710600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr5:68698800-68710600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr5:68699000-68708600	Strong transcription	Dnd41	blood
46	chr5:68699600-68710000	Weak transcription	A549	lung
47	chr5:68699600-68710400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:68699800-68710400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr5:68699800-68710600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr5:68699800-68710600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links