Variant report

Variant	rs2018380
Chromosome Location	chr18:29715321-29715322
allele	A/G
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:
2	chr18:29714493..29716790-chr18:29718511..29720452,2	K562	blood:

Variant related genes	Relation type
ENSG00000263393	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10048285	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10048287	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1054667	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]
rs10853418	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853419	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11081746	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11081747	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11661197	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11663563	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12458837	0.82[EUR][1000 genomes]
rs12458851	0.85[CEU][hapmap];0.94[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs12605137	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1808891	0.85[CEU][hapmap];0.94[GIH][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2010813	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2048245	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	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3980848	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4799326	0.82[CEU][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]
rs4799629	0.82[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs4799632	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4799633	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7238559	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8092272	0.85[ASN][1000 genomes]
rs9676102	0.85[CEU][hapmap];0.94[GIH][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs993897	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2018380	RNF138	cis	Esophagus Mucosa	GTEx
rs2018380	RNF138	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29673800-29715800	Weak transcription	Colonic Mucosa	Colon
2	chr18:29673800-29717000	Weak transcription	HSMMtube	muscle
3	chr18:29675000-29717200	Weak transcription	NH-A	brain
4	chr18:29676800-29717200	Weak transcription	Brain Germinal Matrix	brain
5	chr18:29677000-29715600	Weak transcription	Fetal Heart	heart
6	chr18:29677000-29717000	Weak transcription	Aorta	Aorta
7	chr18:29695800-29717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:29699600-29715400	Weak transcription	Left Ventricle	heart
9	chr18:29705400-29715400	Weak transcription	Fetal Kidney	kidney
10	chr18:29705400-29716400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr18:29705400-29717800	Weak transcription	A549	lung
12	chr18:29706200-29715600	Weak transcription	Fetal Muscle Leg	muscle
13	chr18:29706200-29718600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr18:29707400-29718400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr18:29707800-29717200	Weak transcription	HSMM	muscle
16	chr18:29709200-29717400	Weak transcription	Brain Substantia Nigra	brain
17	chr18:29709200-29718200	Weak transcription	K562	blood
18	chr18:29709200-29718400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr18:29709200-29718800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr18:29709600-29716400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr18:29709600-29719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr18:29710800-29716200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr18:29711600-29718200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr18:29711600-29718400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr18:29712000-29718600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr18:29712200-29715400	Weak transcription	Fetal Brain Female	brain
27	chr18:29712400-29716000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr18:29712400-29716400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr18:29712400-29717200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr18:29712400-29717400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr18:29712400-29718200	Weak transcription	Liver	Liver
32	chr18:29712400-29718400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr18:29712600-29717000	Weak transcription	Fetal Intestine Large	intestine
34	chr18:29712600-29717200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr18:29712600-29717600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr18:29712600-29718600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr18:29713000-29715400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr18:29713600-29716000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr18:29713600-29717200	Weak transcription	GM12878-XiMat	blood
40	chr18:29713600-29717600	Weak transcription	Primary B cells from cord blood	blood
41	chr18:29713600-29718400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr18:29713800-29715400	Weak transcription	Adipose Nuclei	Adipose
43	chr18:29713800-29716800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr18:29713800-29716800	Weak transcription	Fetal Thymus	thymus
45	chr18:29713800-29718200	Weak transcription	Primary T cells from cord blood	blood
46	chr18:29713800-29718400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr18:29714000-29715600	Weak transcription	Fetal Stomach	stomach
48	chr18:29714000-29716200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr18:29714000-29716400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr18:29714200-29718600	Weak transcription	Thymus	Thymus

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