Variant report

Variant	rs10048287
Chromosome Location	chr18:29705724-29705725
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	POLR2A	chr18:29704669-29706078	K562	blood:	n/a	n/a

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
ENSG00000263393	TF binding region
ENSG00000265008	Chromatin interaction
ENSG00000134758	Chromatin interaction
ENSG00000238982	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10048285	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054667	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10853418	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10853419	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11081746	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11081747	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11661197	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11663563	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12458837	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12458851	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12604223	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12605137	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1808891	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2010813	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2018380	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2048245	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3980846	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3980848	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4799632	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4799633	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7238559	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8092272	0.86[ASN][1000 genomes]
rs9676102	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs993897	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10048287	RNF138	cis	Esophagus Mucosa	GTEx
rs10048287	RNF138	cis	multi-tissue	Pritchard
rs10048287	RNF138	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 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	chr18:29676400-29707000	Weak transcription	Brain Angular Gyrus	brain
11	chr18:29676800-29717200	Weak transcription	Brain Germinal Matrix	brain
12	chr18:29677000-29713800	Weak transcription	Small Intestine	intestine
13	chr18:29677000-29715600	Weak transcription	Fetal Heart	heart
14	chr18:29677000-29717000	Weak transcription	Aorta	Aorta
15	chr18:29687200-29713600	Strong transcription	Dnd41	blood
16	chr18:29688200-29706400	Strong transcription	Fetal Thymus	thymus
17	chr18:29688200-29712400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr18:29689400-29713600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr18:29689800-29709400	Weak transcription	Gastric	stomach
20	chr18:29689800-29713200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr18:29690200-29706600	Weak transcription	Right Ventricle	heart
22	chr18:29690800-29710400	Weak transcription	Colon Smooth Muscle	Colon
23	chr18:29691000-29709400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr18:29691000-29712400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr18:29691000-29712600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr18:29691200-29707200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr18:29691200-29713600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr18:29691400-29715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr18:29691600-29713000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr18:29691800-29712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr18:29693200-29710400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr18:29693400-29710400	Weak transcription	Fetal Brain Male	brain
33	chr18:29693600-29706400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr18:29694000-29706200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr18:29695200-29709000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr18:29695200-29713200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr18:29695800-29715200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:29695800-29717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr18:29696000-29708800	Weak transcription	HepG2	liver
40	chr18:29696800-29710200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr18:29696800-29712000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr18:29697000-29714200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr18:29697600-29707800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr18:29698000-29708600	Weak transcription	Brain Substantia Nigra	brain
45	chr18:29699600-29715400	Weak transcription	Left Ventricle	heart
46	chr18:29700000-29707800	Weak transcription	Fetal Stomach	stomach
47	chr18:29700400-29707400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr18:29700400-29709400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr18:29700600-29709200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr18:29700600-29711600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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