Variant report

Variant	rs428598
Chromosome Location	chr18:9595853-9595854
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9594858..9597558-chr18:9614248..9616397,2	MCF-7	breast:
2	chr18:9593651..9596050-chr18:9613258..9616024,2	MCF-7	breast:
3	chr18:9595087..9597869-chr18:9607007..9610720,3	MCF-7	breast:
4	chr18:9593612..9595267-chr18:9595493..9597647,2	K562	blood:

Variant related genes	Relation type
ENSG00000263627	Chromatin interaction
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11081489	0.81[ASN][1000 genomes]
rs1662885	0.89[ASN][1000 genomes]
rs1787165	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787166	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2028661	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028662	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028663	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289684	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs328995	1.00[CHB][hapmap]
rs329002	1.00[ASN][1000 genomes]
rs329004	1.00[ASN][1000 genomes]
rs329008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs329023	0.90[ASN][1000 genomes]
rs329024	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs329033	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35444634	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs583306	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586544	0.81[ASN][1000 genomes]
rs589559	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs599861	1.00[ASN][1000 genomes]
rs610564	0.82[ASN][1000 genomes]
rs62088920	0.81[ASN][1000 genomes]
rs633907	0.85[CHB][hapmap]
rs638578	0.89[ASN][1000 genomes]
rs667695	1.00[ASN][1000 genomes]
rs671339	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677461	0.85[ASN][1000 genomes]
rs680478	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681297	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683319	0.81[ASN][1000 genomes]
rs694861	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7233160	1.00[ASN][1000 genomes]
rs7234128	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7359735	0.87[EUR][1000 genomes]
rs8088389	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8090919	0.89[ASN][1000 genomes]
rs9807577	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9807604	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807610	0.82[EUR][1000 genomes]
rs9807614	0.81[EUR][1000 genomes]
rs9950583	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv543644	chr18:9576145-9612516	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs428598	RP11-692N5.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:9576200-9597800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:9581400-9609200	Weak transcription	Pancreas	Pancrea
5	chr18:9582000-9597000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr18:9582800-9597600	Weak transcription	Fetal Brain Male	brain
7	chr18:9584800-9596600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr18:9585000-9597200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:9588600-9612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr18:9589000-9596800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr18:9589000-9597200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr18:9589000-9597200	Weak transcription	Ovary	ovary
13	chr18:9589000-9608800	Weak transcription	Thymus	Thymus
14	chr18:9589000-9609200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr18:9589000-9611000	Weak transcription	Lung	lung
16	chr18:9589200-9598200	Weak transcription	Primary B cells from cord blood	blood
17	chr18:9589200-9599200	Weak transcription	Fetal Kidney	kidney
18	chr18:9590800-9597600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr18:9591600-9597000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr18:9592000-9597400	Weak transcription	Fetal Brain Female	brain
21	chr18:9592400-9597000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr18:9592400-9599400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr18:9592600-9597000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr18:9592600-9599800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr18:9593000-9598800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr18:9594000-9596600	Weak transcription	Primary T cells from cord blood	blood
27	chr18:9594000-9597200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr18:9594000-9597600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr18:9594000-9599400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr18:9594200-9596400	Enhancers	Fetal Intestine Small	intestine
31	chr18:9594200-9596600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr18:9594200-9597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr18:9594200-9597400	Weak transcription	Brain Germinal Matrix	brain
34	chr18:9594200-9600400	Weak transcription	Placenta	Placenta
35	chr18:9594200-9600400	Weak transcription	Fetal Stomach	stomach
36	chr18:9594200-9600600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr18:9594200-9609200	Weak transcription	Aorta	Aorta
38	chr18:9594200-9613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr18:9594400-9596600	Enhancers	Rectal Smooth Muscle	rectum
40	chr18:9594400-9596800	Enhancers	Colon Smooth Muscle	Colon
41	chr18:9594400-9597000	Weak transcription	Fetal Muscle Leg	muscle
42	chr18:9594400-9597400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr18:9594400-9600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr18:9594600-9596000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:9594600-9596000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr18:9594600-9596000	Enhancers	Adipose Nuclei	Adipose
47	chr18:9594600-9596000	Enhancers	Liver	Liver
48	chr18:9594600-9596000	Enhancers	Left Ventricle	heart
49	chr18:9594600-9596000	Enhancers	Placenta Amnion	Placenta Amnion
50	chr18:9594600-9596000	Enhancers	Small Intestine	intestine

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