Variant report

Variant	rs2048245
Chromosome Location	chr18:29691607-29691608
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	chr18:29686985..29688573-chr18:29689845..29692156,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10048285	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10048287	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054667	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]
rs10853418	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853419	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11081746	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11081747	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11661197	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11663563	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12458548	0.82[AMR][1000 genomes]
rs12458837	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12458851	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12604223	0.81[AMR][1000 genomes]
rs12605137	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1808891	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2010813	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2018380	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3980846	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3980848	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4799326	0.82[CEU][hapmap]
rs4799629	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs4799632	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4799633	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62093949	0.80[AMR][1000 genomes]
rs62093950	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7238559	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]
rs8092272	0.83[ASN][1000 genomes]
rs9676102	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs993897	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9953463	0.80[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2048245	RNF138	cis	Esophagus Mucosa	GTEx
rs2048245	RNF138	Cis_1M	lymphoblastoid	RTeQTL
rs2048245	RNF138	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29673400-29692800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:29673400-29713800	Weak transcription	Spleen	Spleen
3	chr18:29673800-29702000	Weak transcription	Pancreas	Pancrea
4	chr18:29673800-29714000	Weak transcription	Esophagus	oesophagus
5	chr18:29673800-29714200	Weak transcription	Ovary	ovary
6	chr18:29673800-29715200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:29673800-29715200	Weak transcription	Lung	lung
8	chr18:29673800-29715800	Weak transcription	Colonic Mucosa	Colon
9	chr18:29673800-29717000	Weak transcription	HSMMtube	muscle
10	chr18:29674000-29692600	Weak transcription	Placenta	Placenta
11	chr18:29674000-29712000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:29674200-29692800	Weak transcription	HSMM	muscle
13	chr18:29674200-29693000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr18:29674600-29695600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr18:29674600-29703000	Weak transcription	Osteobl	bone
16	chr18:29674600-29705600	Weak transcription	NHLF	lung
17	chr18:29675000-29692200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr18:29675000-29694600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr18:29675000-29717200	Weak transcription	NH-A	brain
20	chr18:29675200-29692800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr18:29675400-29693200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr18:29675400-29693200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr18:29675600-29691800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr18:29675800-29692000	Weak transcription	HMEC	breast
25	chr18:29676000-29693000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr18:29676200-29692000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr18:29676200-29697200	Weak transcription	NHDF-Ad	bronchial
28	chr18:29676400-29691800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr18:29676400-29692200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr18:29676400-29693200	Weak transcription	Fetal Lung	lung
31	chr18:29676400-29707000	Weak transcription	Brain Angular Gyrus	brain
32	chr18:29676600-29692200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr18:29676600-29692200	Weak transcription	NHEK	skin
34	chr18:29676600-29704800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr18:29676800-29691800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr18:29676800-29697400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr18:29676800-29704600	Weak transcription	Fetal Brain Female	brain
38	chr18:29676800-29705000	Weak transcription	Brain Hippocampus Middle	brain
39	chr18:29676800-29717200	Weak transcription	Brain Germinal Matrix	brain
40	chr18:29677000-29691800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr18:29677000-29692200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr18:29677000-29692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr18:29677000-29696800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:29677000-29713800	Weak transcription	Small Intestine	intestine
45	chr18:29677000-29715600	Weak transcription	Fetal Heart	heart
46	chr18:29677000-29717000	Weak transcription	Aorta	Aorta
47	chr18:29677200-29692400	Weak transcription	Left Ventricle	heart
48	chr18:29677400-29694600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr18:29677800-29692200	Weak transcription	Fetal Brain Male	brain
50	chr18:29678200-29692400	Weak transcription	Thymus	Thymus

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