Variant report

Variant	rs1054667
Chromosome Location	chr18:29711261-29711262
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000263393	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10048285	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10048287	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10775450	0.84[CHD][hapmap]
rs10853418	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853419	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11081746	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11081747	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11661197	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11663563	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12458837	0.81[EUR][1000 genomes]
rs12458851	0.87[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs12604223	0.82[AMR][1000 genomes]
rs12605137	0.86[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1808891	0.87[GIH][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2010813	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2018380	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048245	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3980846	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3980848	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4799629	0.82[GIH][hapmap]
rs4799632	0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4799633	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7238559	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]
rs8092272	0.85[ASN][1000 genomes]
rs9676102	0.87[GIH][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs993897	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1054667	RNF138	cis	Esophagus Mucosa	GTEx
rs1054667	RNF138	cis	multi-tissue	Pritchard
rs1054667	RNF138	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

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	chr18:29674000-29712000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr18:29675000-29717200	Weak transcription	NH-A	brain
10	chr18:29676800-29717200	Weak transcription	Brain Germinal Matrix	brain
11	chr18:29677000-29713800	Weak transcription	Small Intestine	intestine
12	chr18:29677000-29715600	Weak transcription	Fetal Heart	heart
13	chr18:29677000-29717000	Weak transcription	Aorta	Aorta
14	chr18:29687200-29713600	Strong transcription	Dnd41	blood
15	chr18:29688200-29712400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:29689400-29713600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr18:29689800-29713200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr18:29691000-29712400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr18:29691000-29712600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr18:29691200-29713600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr18:29691400-29715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr18:29691600-29713000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr18:29691800-29712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr18:29695200-29713200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr18:29695800-29715200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:29695800-29717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr18:29696800-29712000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr18:29697000-29714200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr18:29699600-29715400	Weak transcription	Left Ventricle	heart
30	chr18:29700600-29711600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr18:29701000-29712400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr18:29701800-29712400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr18:29702200-29712200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr18:29702200-29712200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr18:29702200-29712400	Strong transcription	Liver	Liver
36	chr18:29702200-29712600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr18:29702200-29713600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr18:29702400-29712400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr18:29702800-29712400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr18:29702800-29712400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr18:29703200-29712400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr18:29704000-29711600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr18:29704000-29712200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr18:29704000-29713600	Strong transcription	Primary B cells from cord blood	blood
45	chr18:29704200-29714600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr18:29705400-29713800	Weak transcription	Brain Anterior Caudate	brain
47	chr18:29705400-29714000	Weak transcription	Brain Hippocampus Middle	brain
48	chr18:29705400-29714200	Weak transcription	HUVEC	blood vessel
49	chr18:29705400-29715400	Weak transcription	Fetal Kidney	kidney
50	chr18:29705400-29716400	Weak transcription	Stomach Smooth Muscle	stomach

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