Variant report

Variant	rs7238559
Chromosome Location	chr18:29675793-29675794
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr18:29675074-29676117	HEK293	kidney:	n/a	n/a
2	MAFF	chr18:29675777-29676115	HepG2	liver:	n/a	n/a
3	POLR2A	chr18:29675781-29675872	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr18:29671561-29677909	K562	blood:	n/a	n/a
5	MAFK	chr18:29675759-29676115	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29671668..29674127-chr18:29674569..29677601,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265008	TF binding region
ENSG00000265008	Chromatin interaction
ENSG00000134758	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10048285	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10048287	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1054667	0.85[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10853418	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10853419	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11081746	0.82[CEU][hapmap]
rs11081747	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11661197	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11663563	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12458548	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12458837	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12458851	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12605137	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2010813	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2018380	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2048245	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3760568	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3980846	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4799326	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4799629	0.88[AMR][1000 genomes]
rs4799632	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4799633	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62093949	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62093950	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9967524	0.82[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	nsv909523	chr18:29645496-29679922	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1055457	chr18:29654978-29677371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7238559	RNF138	Cis_1M	lymphoblastoid	RTeQTL
rs7238559	RNF138	cis	multi-tissue	Pritchard
rs7238559	RNF138	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29672600-29676000	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr18:29673400-29692800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:29673400-29713800	Weak transcription	Spleen	Spleen
4	chr18:29673600-29678400	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr18:29673800-29675800	Weak transcription	Left Ventricle	heart
6	chr18:29673800-29675800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr18:29673800-29676400	Weak transcription	Aorta	Aorta
8	chr18:29673800-29676400	Enhancers	Brain Angular Gyrus	brain
9	chr18:29673800-29676600	Enhancers	Brain Cingulate Gyrus	brain
10	chr18:29673800-29676600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr18:29673800-29676600	Enhancers	Brain Substantia Nigra	brain
12	chr18:29673800-29676800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr18:29673800-29677000	Enhancers	Fetal Heart	heart
14	chr18:29673800-29678000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr18:29673800-29679400	Weak transcription	Gastric	stomach
16	chr18:29673800-29702000	Weak transcription	Pancreas	Pancrea
17	chr18:29673800-29714000	Weak transcription	Esophagus	oesophagus
18	chr18:29673800-29714200	Weak transcription	Ovary	ovary
19	chr18:29673800-29715200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr18:29673800-29715200	Weak transcription	Lung	lung
21	chr18:29673800-29715800	Weak transcription	Colonic Mucosa	Colon
22	chr18:29673800-29717000	Weak transcription	HSMMtube	muscle
23	chr18:29674000-29676000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr18:29674000-29676000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr18:29674000-29676400	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr18:29674000-29677400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr18:29674000-29679000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr18:29674000-29679600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr18:29674000-29689200	Weak transcription	Right Atrium	heart
30	chr18:29674000-29692600	Weak transcription	Placenta	Placenta
31	chr18:29674000-29712000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr18:29674200-29676400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr18:29674200-29676400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr18:29674200-29677800	Genic enhancers	Primary monocytes fromperipheralblood	blood
35	chr18:29674200-29692800	Weak transcription	HSMM	muscle
36	chr18:29674200-29693000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr18:29674400-29676000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr18:29674400-29676000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
39	chr18:29674400-29676600	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr18:29674400-29677000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr18:29674400-29678400	Genic enhancers	Fetal Thymus	thymus
42	chr18:29674400-29679400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr18:29674600-29675800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr18:29674600-29675800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr18:29674600-29676600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr18:29674600-29676800	Enhancers	Brain Germinal Matrix	brain
47	chr18:29674600-29676800	Weak transcription	Fetal Kidney	kidney
48	chr18:29674600-29677000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr18:29674600-29677000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr18:29674600-29677200	Genic enhancers	Primary B cells from cord blood	blood

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