Variant report

Variant	rs4239374
Chromosome Location	chr18:29702225-29702226
allele	C/T
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	FOXA2	chr18:29702027-29702383	A549	lung:	n/a	chr18:29702278-29702290
2	FOXA1	chr18:29702021-29702324	HepG2	liver:	n/a	chr18:29702276-29702291 chr18:29702243-29702258 chr18:29702278-29702290
3	TBP	chr18:29701963-29702318	K562	blood:	n/a	n/a
4	FOXA2	chr18:29702062-29702380	HepG2	liver:	n/a	chr18:29702278-29702290
5	FOXA1	chr18:29701973-29702484	HepG2	liver:	n/a	chr18:29702276-29702291 chr18:29702243-29702258 chr18:29702278-29702290
6	FOXA1	chr18:29702023-29702465	HepG2	liver:	n/a	chr18:29702276-29702291 chr18:29702243-29702258 chr18:29702278-29702290
7	TAL1	chr18:29702065-29702296	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29670755..29674701-chr18:29702072..29706406,4	K562	blood:
2	chr18:29700311..29703137-chr18:29703186..29705251,2	K562	blood:

Variant related genes	Relation type
RNF138	TF binding region
ENSG00000238982	Chromatin interaction
ENSG00000265008	Chromatin interaction
ENSG00000263393	Chromatin interaction
ENSG00000134758	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs16962699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16962701	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs1834162	0.85[ASN][1000 genomes]
rs4799327	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs4799328	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs4799630	0.82[ASN][1000 genomes]
rs55786778	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56273402	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56360277	0.84[ASN][1000 genomes]
rs56810557	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58425259	0.85[ASN][1000 genomes]
rs67074695	0.86[ASN][1000 genomes]
rs68037424	0.84[ASN][1000 genomes]
rs7229437	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs7230167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7234604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73415858	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73415859	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73415860	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4239374	RNF138	cis	lymphoblastoid	seeQTL

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	chr18:29674600-29703000	Weak transcription	Osteobl	bone
10	chr18:29674600-29705600	Weak transcription	NHLF	lung
11	chr18:29675000-29717200	Weak transcription	NH-A	brain
12	chr18:29676400-29707000	Weak transcription	Brain Angular Gyrus	brain
13	chr18:29676600-29704800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr18:29676800-29704600	Weak transcription	Fetal Brain Female	brain
15	chr18:29676800-29705000	Weak transcription	Brain Hippocampus Middle	brain
16	chr18:29676800-29717200	Weak transcription	Brain Germinal Matrix	brain
17	chr18:29677000-29713800	Weak transcription	Small Intestine	intestine
18	chr18:29677000-29715600	Weak transcription	Fetal Heart	heart
19	chr18:29677000-29717000	Weak transcription	Aorta	Aorta
20	chr18:29687200-29713600	Strong transcription	Dnd41	blood
21	chr18:29688200-29706400	Strong transcription	Fetal Thymus	thymus
22	chr18:29688200-29712400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:29689400-29704600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr18:29689400-29713600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr18:29689800-29705000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr18:29689800-29709400	Weak transcription	Gastric	stomach
27	chr18:29689800-29713200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr18:29690200-29706600	Weak transcription	Right Ventricle	heart
29	chr18:29690400-29704800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr18:29690800-29710400	Weak transcription	Colon Smooth Muscle	Colon
31	chr18:29691000-29709400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr18:29691000-29712400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:29691000-29712600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr18:29691200-29707200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr18:29691200-29713600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr18:29691400-29715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr18:29691600-29713000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr18:29691800-29712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr18:29692000-29703000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr18:29692600-29702400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr18:29693200-29710400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr18:29693400-29704600	Weak transcription	Brain Anterior Caudate	brain
43	chr18:29693400-29710400	Weak transcription	Fetal Brain Male	brain
44	chr18:29693600-29706400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr18:29694000-29704600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr18:29694000-29704600	Weak transcription	A549	lung
47	chr18:29694000-29706200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr18:29694800-29704000	Weak transcription	HMEC	breast
49	chr18:29695000-29704800	Weak transcription	Fetal Kidney	kidney
50	chr18:29695200-29704000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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