Variant report

Variant	rs4799326
Chromosome Location	chr18:29665863-29665864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:29662644..29667608-chr18:29668028..29673014,9	K562	blood:
2	chr18:29660336..29661951-chr18:29664954..29667841,2	K562	blood:
3	chr18:29661516..29666367-chr18:29670429..29672911,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134758	Chromatin interaction
ENSG00000265008	Chromatin interaction

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

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

rs_ID	r²[population]
rs11081741	0.82[CEU][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs11081746	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11663563	0.86[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs12458548	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12458837	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12458851	0.96[CEU][hapmap];0.92[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12605137	0.86[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs1808891	0.96[CEU][hapmap];0.92[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs2018380	0.82[CEU][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]
rs2048245	0.82[CEU][hapmap]
rs3760568	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3980848	0.80[AMR][1000 genomes]
rs4799629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4799632	0.84[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs62093949	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62093950	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7238559	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9676102	0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs993897	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757673	chr18:29632749-29674992	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2758719	chr18:29632749-29674992	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv909520	chr18:29645496-29666127	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv909521	chr18:29645496-29671510	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv909522	chr18:29645496-29674992	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv909523	chr18:29645496-29679922	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1055457	chr18:29654978-29677371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4799326	RNF138	cis	Esophagus Mucosa	GTEx
rs4799326	RNF138	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29631400-29671400	Weak transcription	Hela-S3	cervix
2	chr18:29656000-29671400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr18:29663800-29671400	Weak transcription	Fetal Kidney	kidney
4	chr18:29664400-29666000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr18:29664400-29666000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr18:29664400-29666000	Enhancers	NH-A	brain
7	chr18:29664400-29666200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr18:29664400-29666200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr18:29664400-29666400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr18:29664400-29666400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr18:29664400-29666600	Enhancers	Fetal Thymus	thymus
12	chr18:29664400-29671400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr18:29664600-29666400	Enhancers	Thymus	Thymus
14	chr18:29664600-29667600	Enhancers	NHEK	skin
15	chr18:29664600-29671600	Weak transcription	Left Ventricle	heart
16	chr18:29664800-29666000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr18:29664800-29666000	Enhancers	HMEC	breast
18	chr18:29665000-29666000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr18:29665000-29666000	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr18:29665000-29666000	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr18:29665000-29666000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr18:29665000-29666000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr18:29665000-29666000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr18:29665000-29666000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr18:29665000-29666000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr18:29665000-29666000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr18:29665000-29666000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr18:29665000-29666000	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr18:29665000-29666200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr18:29665000-29666200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr18:29665000-29666200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr18:29665000-29666400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr18:29665200-29666000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr18:29665200-29666000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr18:29665200-29666400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr18:29665200-29666400	Weak transcription	Fetal Muscle Leg	muscle
37	chr18:29665200-29671400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr18:29665200-29671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr18:29665400-29666000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr18:29665400-29666000	Active TSS	Stomach Mucosa	stomach
41	chr18:29665400-29666000	Enhancers	NHDF-Ad	bronchial
42	chr18:29665400-29666200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr18:29665400-29667600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr18:29665400-29671400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr18:29665600-29666000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr18:29665600-29666000	Flanking Active TSS	Dnd41	blood
47	chr18:29665600-29666000	Flanking Active TSS	GM12878-XiMat	blood
48	chr18:29665600-29666000	Flanking Active TSS	HUVEC	blood vessel
49	chr18:29665600-29666200	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr18:29665600-29666600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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