Variant report

Variant	rs993897
Chromosome Location	chr18:29713665-29713666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29703390..29707950-chr18:29711661..29715023,4	K562	blood:
2	chr18:29703952..29707950-chr18:29710554..29715618,4	K562	blood:

Variant related genes	Relation type
ENSG00000134758	Chromatin interaction
ENSG00000263393	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10048285	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10048287	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1054667	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10853418	0.80[EUR][1000 genomes]
rs11081746	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11081747	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11081750	0.88[ASN][1000 genomes]
rs11663563	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12454857	0.88[ASN][1000 genomes]
rs12455044	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12457134	0.81[ASN][1000 genomes]
rs12458548	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12458837	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12458851	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12604223	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12605137	0.83[EUR][1000 genomes]
rs1808891	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010813	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2018380	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2048245	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3760568	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3980846	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3980848	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799326	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4799629	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4799633	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62093949	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62093950	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62095576	0.81[ASN][1000 genomes]
rs62095578	0.88[ASN][1000 genomes]
rs62095579	0.88[ASN][1000 genomes]
rs62095587	0.87[ASN][1000 genomes]
rs67929870	0.88[ASN][1000 genomes]
rs7232533	0.87[ASN][1000 genomes]
rs7240197	0.82[ASN][1000 genomes]
rs72639475	0.88[ASN][1000 genomes]
rs9676102	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944759	0.88[ASN][1000 genomes]
rs9944778	0.88[ASN][1000 genomes]
rs9952622	0.88[ASN][1000 genomes]
rs9955753	0.85[ASN][1000 genomes]
rs9964960	0.88[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	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs993897	RNF138	cis	multi-tissue	Pritchard
rs993897	RNF138	cis	Esophagus Mucosa	GTEx
rs993897	RNF138	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29673400-29713800	Weak transcription	Spleen	Spleen
2	chr18:29673800-29714000	Weak transcription	Esophagus	oesophagus
3	chr18:29673800-29714200	Weak transcription	Ovary	ovary
4	chr18:29673800-29715200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:29673800-29715200	Weak transcription	Lung	lung
6	chr18:29673800-29715800	Weak transcription	Colonic Mucosa	Colon
7	chr18:29673800-29717000	Weak transcription	HSMMtube	muscle
8	chr18:29675000-29717200	Weak transcription	NH-A	brain
9	chr18:29676800-29717200	Weak transcription	Brain Germinal Matrix	brain
10	chr18:29677000-29713800	Weak transcription	Small Intestine	intestine
11	chr18:29677000-29715600	Weak transcription	Fetal Heart	heart
12	chr18:29677000-29717000	Weak transcription	Aorta	Aorta
13	chr18:29691400-29715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr18:29695800-29715200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:29695800-29717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr18:29697000-29714200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr18:29699600-29715400	Weak transcription	Left Ventricle	heart
18	chr18:29704200-29714600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr18:29705400-29713800	Weak transcription	Brain Anterior Caudate	brain
20	chr18:29705400-29714000	Weak transcription	Brain Hippocampus Middle	brain
21	chr18:29705400-29714200	Weak transcription	HUVEC	blood vessel
22	chr18:29705400-29715400	Weak transcription	Fetal Kidney	kidney
23	chr18:29705400-29716400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr18:29705400-29717800	Weak transcription	A549	lung
25	chr18:29705600-29713800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr18:29705800-29715200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr18:29706200-29715200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr18:29706200-29715600	Weak transcription	Fetal Muscle Leg	muscle
29	chr18:29706200-29718600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr18:29706800-29713800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr18:29707200-29715200	Weak transcription	Fetal Lung	lung
32	chr18:29707400-29718400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr18:29707800-29717200	Weak transcription	HSMM	muscle
34	chr18:29708000-29715000	Weak transcription	Placenta	Placenta
35	chr18:29708800-29715000	Weak transcription	Pancreas	Pancrea
36	chr18:29709200-29717400	Weak transcription	Brain Substantia Nigra	brain
37	chr18:29709200-29718200	Weak transcription	K562	blood
38	chr18:29709200-29718400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr18:29709200-29718800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr18:29709600-29716400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr18:29709600-29719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr18:29710000-29713800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr18:29710800-29714600	Weak transcription	Osteobl	bone
44	chr18:29710800-29716200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr18:29711000-29713800	Strong transcription	Fetal Thymus	thymus
46	chr18:29711400-29714400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr18:29711600-29714000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr18:29711600-29718200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr18:29711600-29718400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr18:29711800-29714000	Strong transcription	Duodenum Mucosa	Duodenum

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