Variant report

Variant	rs4902339
Chromosome Location	chr14:65394290-65394291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65380579..65384480-chr14:65390113..65394782,6	MCF-7	breast:
2	chr14:65379584..65383779-chr14:65391377..65398715,8	MCF-7	breast:
3	chr14:65389456..65391707-chr14:65393216..65394739,2	K562	blood:

Variant related genes	Relation type
ENSG00000125954	Chromatin interaction
ENSG00000258289	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10136196	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10145845	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1064108	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11540873	0.85[EUR][1000 genomes]
rs11622394	0.80[AFR][1000 genomes]
rs11627589	0.94[AFR][1000 genomes]
rs11627688	0.82[AFR][1000 genomes]
rs11848113	0.80[AFR][1000 genomes]
rs12433639	0.92[AFR][1000 genomes]
rs12433641	0.92[AFR][1000 genomes]
rs12436747	0.80[AFR][1000 genomes]
rs12590986	0.82[AFR][1000 genomes]
rs12878229	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12878467	0.82[AFR][1000 genomes]
rs12879744	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12881353	0.82[AFR][1000 genomes]
rs12889323	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12889417	0.82[AFR][1000 genomes]
rs12890654	0.82[AFR][1000 genomes]
rs12891652	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12897440	0.82[AFR][1000 genomes]
rs1951487	0.82[AFR][1000 genomes]
rs1951488	0.82[AFR][1000 genomes]
rs1951993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1957417	0.82[AFR][1000 genomes]
rs1957418	0.92[AFR][1000 genomes]
rs1957419	0.82[AFR][1000 genomes]
rs1957421	0.82[AFR][1000 genomes]
rs1957423	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1957425	0.82[AFR][1000 genomes]
rs2071566	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2147612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2147616	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277501	0.81[ASN][1000 genomes]
rs2296326	0.81[ASN][1000 genomes]
rs2357868	0.82[AFR][1000 genomes]
rs2412106	0.81[AMR][1000 genomes]
rs2737844	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2898874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087955	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34201584	0.80[AFR][1000 genomes]
rs34969442	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35176965	0.92[AFR][1000 genomes]
rs3759681	0.87[EUR][1000 genomes]
rs4243629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45454295	0.88[EUR][1000 genomes]
rs4902334	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6573585	0.82[AFR][1000 genomes]
rs7143358	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7151780	0.82[AFR][1000 genomes]
rs743263	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs762071	0.86[AFR][1000 genomes]
rs8003530	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8016174	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8021590	0.85[AFR][1000 genomes]
rs8021876	0.82[AFR][1000 genomes]
rs8021998	0.82[AFR][1000 genomes]
rs8022122	0.82[AFR][1000 genomes]

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4902339	RAB15	Cis_1M	lymphoblastoid	RTeQTL
rs4902339	CHURC1	cis	Esophagus Mucosa	GTEx
rs4902339	CHURC1	cis	Nerve Tibial	GTEx
rs4902339	CHURC1	Cis_1M	lymphoblastoid	RTeQTL
rs4902339	CHURC1	cis	Heart Left Ventricle	GTEx
rs4902339	CHURC1	cis	Esophagus Muscularis	GTEx
rs4902339	CHURC1	cis	Artery Tibial	GTEx
rs4902339	CHURC1	cis	Skin Sun Exposed Lower leg	GTEx
rs4902339	CHURC1	cis	lung	GTEx
rs4902339	CHURC1	cis	multi-tissue	Pritchard
rs4902339	CHURC1	cis	Adipose Subcutaneous	GTEx
rs4902339	CHURC1	cis	Thyroid	GTEx
rs4902339	CHURC1	cis	Artery Aorta	GTEx
rs4902339	CHURC1	cis	Whole Blood	GTEx
rs4902339	CHURC1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65382000-65399200	Weak transcription	Esophagus	oesophagus
2	chr14:65382000-65409200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:65382200-65394800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:65382200-65395600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:65382400-65409200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr14:65382400-65417400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr14:65382400-65420000	Weak transcription	Fetal Brain Male	brain
8	chr14:65382800-65394400	Weak transcription	Small Intestine	intestine
9	chr14:65382800-65394600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:65382800-65404200	Weak transcription	Stomach Mucosa	stomach
11	chr14:65383000-65394800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:65383000-65419400	Weak transcription	K562	blood
13	chr14:65383800-65403800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr14:65384400-65404800	Weak transcription	Gastric	stomach
15	chr14:65385600-65395800	Weak transcription	Pancreas	Pancrea
16	chr14:65386400-65409200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr14:65387400-65395800	Weak transcription	Aorta	Aorta
18	chr14:65388400-65394600	Strong transcription	Fetal Thymus	thymus
19	chr14:65389400-65394400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr14:65389400-65395000	Strong transcription	Primary B cells from cord blood	blood
21	chr14:65390000-65396400	Strong transcription	HSMM	muscle
22	chr14:65390200-65399200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:65390400-65396200	Strong transcription	Liver	Liver
24	chr14:65390400-65398000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr14:65390600-65394400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr14:65390600-65394600	Genic enhancers	Primary T cells from cord blood	blood
27	chr14:65390600-65395000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr14:65390600-65395200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr14:65390600-65395800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr14:65390600-65396000	Strong transcription	Brain Anterior Caudate	brain
31	chr14:65390600-65396200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr14:65390600-65396200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr14:65390600-65396200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr14:65390600-65396200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr14:65390600-65396400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr14:65390600-65396600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr14:65390600-65396600	Strong transcription	Fetal Muscle Leg	muscle
38	chr14:65390600-65397200	Strong transcription	Fetal Intestine Large	intestine
39	chr14:65390600-65398000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:65390600-65400400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr14:65390600-65400600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr14:65390600-65401800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr14:65390600-65409600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr14:65390600-65409800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr14:65390800-65395000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr14:65390800-65395000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr14:65390800-65395400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr14:65390800-65395600	Strong transcription	Colon Smooth Muscle	Colon
49	chr14:65390800-65396000	Strong transcription	Brain Angular Gyrus	brain
50	chr14:65390800-65396000	Strong transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links