Variant report

Variant	rs3859302
Chromosome Location	chr18:13515861-13515862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:13504939..13506992-chr18:13515304..13518121,2	MCF-7	breast:
2	chr18:13513801..13516258-chr18:13517871..13519966,2	MCF-7	breast:
3	chr18:13514331..13515883-chr18:13541189..13543020,2	MCF-7	breast:
4	chr18:13514493..13516094-chr18:13537617..13539462,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNMT-4	chr18:13514519-13516102	NONHSAT058443
2	lnc-FAM210A-4	chr18:13514519-13516106	ENSG00000267136.1

No data

Variant related genes	Relation type
ENSG00000168675	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10163734	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853235	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853236	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12458741	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12607174	0.80[ASN][1000 genomes]
rs12955640	0.94[ASN][1000 genomes]
rs1648585	0.94[ASN][1000 genomes]
rs1648586	0.94[ASN][1000 genomes]
rs1648587	0.94[ASN][1000 genomes]
rs1648588	0.80[ASN][1000 genomes]
rs1648593	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1785151	0.94[ASN][1000 genomes]
rs1785152	0.94[ASN][1000 genomes]
rs1785205	0.94[ASN][1000 genomes]
rs1940914	0.80[ASN][1000 genomes]
rs1940915	0.80[ASN][1000 genomes]
rs1940916	0.80[ASN][1000 genomes]
rs1940918	0.80[ASN][1000 genomes]
rs2027682	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027683	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163445	0.81[ASN][1000 genomes]
rs28415200	0.80[ASN][1000 genomes]
rs28553871	0.80[ASN][1000 genomes]
rs28767549	0.80[ASN][1000 genomes]
rs3097643	0.80[ASN][1000 genomes]
rs3132835	0.80[ASN][1000 genomes]
rs4796988	0.80[ASN][1000 genomes]
rs6505818	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505819	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505820	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505821	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6505822	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7227383	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7229109	0.80[ASN][1000 genomes]
rs7230189	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7230276	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7233826	0.80[ASN][1000 genomes]
rs7234676	0.80[ASN][1000 genomes]
rs7239669	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7240391	0.80[ASN][1000 genomes]
rs7240795	0.80[ASN][1000 genomes]
rs7240821	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7240858	0.80[ASN][1000 genomes]
rs7241010	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7241766	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505922	0.80[ASN][1000 genomes]
rs8088361	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091197	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091352	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8092166	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952307	0.80[ASN][1000 genomes]
rs9958211	0.80[ASN][1000 genomes]
rs9958308	0.80[ASN][1000 genomes]
rs9958406	0.80[ASN][1000 genomes]
rs9958516	0.80[ASN][1000 genomes]
rs9958760	0.80[ASN][1000 genomes]

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:61 , 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	chr18:13500000-13516800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr18:13500400-13517400	Weak transcription	Spleen	Spleen
6	chr18:13501400-13518200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr18:13501600-13525000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:13501800-13530600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr18:13502800-13525200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr18:13503000-13517000	Weak transcription	Adipose Nuclei	Adipose
11	chr18:13503000-13519200	Weak transcription	Pancreas	Pancrea
12	chr18:13503200-13517200	Weak transcription	Fetal Lung	lung
13	chr18:13503200-13521000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr18:13503400-13517400	Weak transcription	Aorta	Aorta
15	chr18:13505000-13536000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr18:13507000-13516200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr18:13507000-13536400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr18:13511600-13530400	Weak transcription	Colon Smooth Muscle	Colon
19	chr18:13512000-13518200	Weak transcription	Brain Hippocampus Middle	brain
20	chr18:13512200-13521600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr18:13512400-13516200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr18:13512600-13516200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr18:13512800-13518400	Strong transcription	Dnd41	blood
24	chr18:13513200-13516000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr18:13513200-13516600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr18:13513200-13516800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr18:13513200-13516800	Weak transcription	Fetal Stomach	stomach
28	chr18:13513200-13517000	Weak transcription	Brain Germinal Matrix	brain
29	chr18:13513200-13517200	Weak transcription	Fetal Brain Female	brain
30	chr18:13513200-13520000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr18:13513200-13526600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr18:13513200-13538200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr18:13513400-13523800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr18:13513600-13517600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr18:13513600-13517600	Weak transcription	Fetal Intestine Large	intestine
36	chr18:13513600-13519400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr18:13513800-13516000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr18:13513800-13520200	Strong transcription	Primary T cells from cord blood	blood
39	chr18:13513800-13520200	Weak transcription	Left Ventricle	heart
40	chr18:13514000-13516200	Weak transcription	Liver	Liver
41	chr18:13514000-13516400	Strong transcription	Fetal Thymus	thymus
42	chr18:13514000-13520000	Weak transcription	Fetal Heart	heart
43	chr18:13514000-13520200	Weak transcription	Psoas Muscle	Psoas
44	chr18:13514000-13523800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr18:13514200-13517200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr18:13514200-13517200	Strong transcription	Thymus	Thymus
47	chr18:13514200-13517800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr18:13514200-13519200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr18:13514400-13519000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr18:13514600-13517800	Strong transcription	Primary neutrophils fromperipheralblood	blood

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