Variant report

Variant	rs7239669
Chromosome Location	chr18:13522062-13522063
allele	A/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	GATA1	chr18:13521759-13522770	PBDE	blood:	n/a	chr18:13521862-13521873

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNMT-4	chr18:13519726-13522887	NONHSAT058443
2	lnc-FAM210A-4	chr18:13519731-13522887	ENSG00000267136.1

Variant related genes	Relation type
ENSG00000272746	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10163734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10853235	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10853236	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12458741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12604898	0.82[JPT][hapmap]
rs12607174	0.88[JPT][hapmap]
rs12955640	0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1648585	0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1648586	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1648587	0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1648588	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1648593	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1785151	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1785152	0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs1785181	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1785205	0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1812468	0.82[JPT][hapmap]
rs1940916	0.88[JPT][hapmap]
rs2027682	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2027683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097643	0.88[JPT][hapmap]
rs3132835	0.88[JPT][hapmap]
rs3859302	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4121593	0.83[JPT][hapmap]
rs4121594	0.81[JPT][hapmap]
rs4796988	0.88[JPT][hapmap]
rs6505818	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505819	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505820	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505821	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6505822	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7227383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7230189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7230276	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7240391	0.88[JPT][hapmap]
rs7240821	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7240858	0.88[JPT][hapmap]
rs7241010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7241766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8088361	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8091197	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8091352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8092166	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9952307	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531246	chr18:13298774-14082028	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1827877	chr18:13511622-13523462	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13471000-13537400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr18:13499600-13539200	Weak transcription	Gastric	stomach
3	chr18:13499800-13531000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr18:13501600-13525000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr18:13501800-13530600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr18:13502800-13525200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr18:13505000-13536000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr18:13507000-13536400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr18:13511600-13530400	Weak transcription	Colon Smooth Muscle	Colon
10	chr18:13513200-13526600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr18:13513200-13538200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr18:13513400-13523800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr18:13514000-13523800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr18:13517000-13532400	Weak transcription	HepG2	liver
15	chr18:13517400-13525000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr18:13517600-13523200	Weak transcription	Primary B cells from cord blood	blood
17	chr18:13517600-13523600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr18:13517600-13523600	Weak transcription	Spleen	Spleen
19	chr18:13517600-13524800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr18:13517600-13526200	Weak transcription	Brain Germinal Matrix	brain
21	chr18:13517600-13526800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr18:13517600-13532800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr18:13517600-13539000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr18:13517600-13539200	Weak transcription	Aorta	Aorta
25	chr18:13517800-13523000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr18:13517800-13525000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr18:13517800-13530200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr18:13518200-13525400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr18:13519000-13523600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr18:13519000-13525200	Weak transcription	Fetal Brain Female	brain
31	chr18:13519000-13527000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:13519000-13529200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr18:13519000-13530200	Weak transcription	Fetal Lung	lung
34	chr18:13519200-13522400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr18:13519200-13523400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr18:13519400-13522400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr18:13519400-13527000	Weak transcription	Fetal Stomach	stomach
38	chr18:13520000-13522800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr18:13520000-13523000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr18:13520200-13522200	Weak transcription	Dnd41	blood
41	chr18:13520200-13522600	Weak transcription	Primary T cells from cord blood	blood
42	chr18:13520200-13522600	Enhancers	Psoas Muscle	Psoas
43	chr18:13520400-13529200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr18:13520600-13524800	Weak transcription	Fetal Heart	heart
45	chr18:13520600-13530400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr18:13521000-13522800	Enhancers	Brain Anterior Caudate	brain
47	chr18:13521000-13523000	Weak transcription	Thymus	Thymus
48	chr18:13521200-13524600	Weak transcription	Left Ventricle	heart
49	chr18:13521200-13530200	Weak transcription	Adipose Nuclei	Adipose
50	chr18:13521400-13522200	Weak transcription	Fetal Thymus	thymus

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