Variant report

Variant	rs12604223
Chromosome Location	chr18:29703739-29703740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29672647..29674860-chr18:29703384..29706167,2	MCF-7	breast:
2	chr18:29670755..29674701-chr18:29702072..29706406,4	K562	blood:

Variant related genes	Relation type
ENSG00000134758	Chromatin interaction
ENSG00000238982	Chromatin interaction
ENSG00000265008	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10048285	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10048287	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1054667	0.82[AMR][1000 genomes]
rs10853418	0.84[AMR][1000 genomes]
rs11081746	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11663563	0.81[AMR][1000 genomes]
rs12455044	0.83[ASN][1000 genomes]
rs12458837	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12458851	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1808891	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2048245	0.81[AMR][1000 genomes]
rs3760568	0.82[AMR][1000 genomes]
rs3980846	0.81[AMR][1000 genomes]
rs3980848	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4799629	0.80[AMR][1000 genomes]
rs62093949	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62093950	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9676102	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs993897	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12604223	RNF138	cis	Esophagus Mucosa	GTEx
rs12604223	RNF138	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr18:29674600-29705600	Weak transcription	NHLF	lung
10	chr18:29675000-29717200	Weak transcription	NH-A	brain
11	chr18:29676400-29707000	Weak transcription	Brain Angular Gyrus	brain
12	chr18:29676600-29704800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr18:29676800-29704600	Weak transcription	Fetal Brain Female	brain
14	chr18:29676800-29705000	Weak transcription	Brain Hippocampus Middle	brain
15	chr18:29676800-29717200	Weak transcription	Brain Germinal Matrix	brain
16	chr18:29677000-29713800	Weak transcription	Small Intestine	intestine
17	chr18:29677000-29715600	Weak transcription	Fetal Heart	heart
18	chr18:29677000-29717000	Weak transcription	Aorta	Aorta
19	chr18:29687200-29713600	Strong transcription	Dnd41	blood
20	chr18:29688200-29706400	Strong transcription	Fetal Thymus	thymus
21	chr18:29688200-29712400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:29689400-29704600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr18:29689400-29713600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr18:29689800-29705000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr18:29689800-29709400	Weak transcription	Gastric	stomach
26	chr18:29689800-29713200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr18:29690200-29706600	Weak transcription	Right Ventricle	heart
28	chr18:29690400-29704800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr18:29690800-29710400	Weak transcription	Colon Smooth Muscle	Colon
30	chr18:29691000-29709400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr18:29691000-29712400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr18:29691000-29712600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr18:29691200-29707200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr18:29691200-29713600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr18:29691400-29715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr18:29691600-29713000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr18:29691800-29712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr18:29693200-29710400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr18:29693400-29704600	Weak transcription	Brain Anterior Caudate	brain
40	chr18:29693400-29710400	Weak transcription	Fetal Brain Male	brain
41	chr18:29693600-29706400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr18:29694000-29704600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr18:29694000-29704600	Weak transcription	A549	lung
44	chr18:29694000-29706200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr18:29694800-29704000	Weak transcription	HMEC	breast
46	chr18:29695000-29704800	Weak transcription	Fetal Kidney	kidney
47	chr18:29695200-29704000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr18:29695200-29709000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr18:29695200-29713200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr18:29695800-29715200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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