Variant report

Variant	rs4799628
Chromosome Location	chr18:29666127-29666128
allele	C/T
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: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10775450	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2063288	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28378426	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4799325	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799631	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61392417	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs627346	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs8085407	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8094028	0.87[CEU][hapmap]
rs8095867	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs889888	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9953463	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9955978	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9962565	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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
rs4799628	RNF138	Cis_1M	lymphoblastoid	RTeQTL
rs4799628	RNF138	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 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	chr18:29664400-29666200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr18:29664400-29666200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr18:29664400-29666400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr18:29664400-29666400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr18:29664400-29666600	Enhancers	Fetal Thymus	thymus
9	chr18:29664400-29671400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr18:29664600-29666400	Enhancers	Thymus	Thymus
11	chr18:29664600-29667600	Enhancers	NHEK	skin
12	chr18:29664600-29671600	Weak transcription	Left Ventricle	heart
13	chr18:29665000-29666200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr18:29665000-29666200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr18:29665000-29666200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr18:29665000-29666400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr18:29665200-29666400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr18:29665200-29666400	Weak transcription	Fetal Muscle Leg	muscle
19	chr18:29665200-29671400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr18:29665200-29671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr18:29665400-29666200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr18:29665400-29667600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:29665400-29671400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr18:29665600-29666200	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr18:29665600-29666600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr18:29665600-29671400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr18:29665600-29671400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:29665800-29666400	Enhancers	Primary B cells from peripheral blood	blood
29	chr18:29665800-29666400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr18:29665800-29666600	Enhancers	NHLF	lung
31	chr18:29665800-29667000	Weak transcription	Osteobl	bone
32	chr18:29665800-29668000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr18:29666000-29666200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr18:29666000-29666200	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr18:29666000-29666200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr18:29666000-29666200	Enhancers	GM12878-XiMat	blood
37	chr18:29666000-29666400	Enhancers	Primary T cells from cord blood	blood
38	chr18:29666000-29666400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr18:29666000-29666400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr18:29666000-29666400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr18:29666000-29666400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr18:29666000-29666400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr18:29666000-29666400	Enhancers	Adipose Nuclei	Adipose
44	chr18:29666000-29666400	Enhancers	Duodenum Mucosa	Duodenum
45	chr18:29666000-29666400	Enhancers	Dnd41	blood
46	chr18:29666000-29666400	Enhancers	HUVEC	blood vessel
47	chr18:29666000-29666600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr18:29666000-29666600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr18:29666000-29666600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr18:29666000-29666600	Enhancers	Primary T helper cells fromperipheralblood	blood

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