Variant report

Variant	rs28718304
Chromosome Location	chr18:44632830-44632831
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44631824..44634440-chr18:44636514..44640477,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KATNAL2-5	chr18:44632317-44634433	ENSG00000267724.1

Variant related genes	Relation type
ENSG00000167220	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12953864	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12968552	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13381713	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1434529	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16954921	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16954999	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1836259	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2289133	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2571002	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571004	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2571005	0.86[EUR][1000 genomes]
rs2571006	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2571007	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2571008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571010	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571014	0.83[EUR][1000 genomes]
rs2571017	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2576052	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2576057	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576058	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635051	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635054	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635056	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2668758	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2668759	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2668761	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668762	0.88[EUR][1000 genomes]
rs2668763	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668784	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2684819	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2684833	0.86[EUR][1000 genomes]
rs2684851	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55730206	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7239323	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8085634	0.94[EUR][1000 genomes]
rs9951617	0.81[EUR][1000 genomes]
rs9953157	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9956809	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9961383	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9962436	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44607600-44637600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr18:44609200-44638400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:44611000-44633000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr18:44611400-44633000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr18:44611600-44635600	Weak transcription	Psoas Muscle	Psoas
6	chr18:44613800-44638200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr18:44617200-44635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:44620600-44635000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr18:44620800-44675400	Weak transcription	A549	lung
10	chr18:44621200-44634800	Weak transcription	Pancreas	Pancrea
11	chr18:44621400-44638600	Weak transcription	Colonic Mucosa	Colon
12	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
13	chr18:44622000-44633200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr18:44622400-44633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:44623000-44637400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr18:44623200-44635200	Weak transcription	HepG2	liver
17	chr18:44623800-44635000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr18:44624200-44634800	Weak transcription	Gastric	stomach
19	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
20	chr18:44624400-44637400	Weak transcription	HMEC	breast
21	chr18:44624400-44640600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr18:44624600-44635000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr18:44626800-44633000	Weak transcription	Placenta	Placenta
25	chr18:44626800-44634600	Weak transcription	NHEK	skin
26	chr18:44626800-44637400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr18:44627000-44633600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr18:44627000-44635000	Weak transcription	Brain Germinal Matrix	brain
29	chr18:44627000-44636600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr18:44627200-44635200	Weak transcription	Fetal Intestine Small	intestine
31	chr18:44627200-44638000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr18:44627600-44633600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr18:44628200-44640200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr18:44628400-44637800	Weak transcription	GM12878-XiMat	blood
35	chr18:44628600-44633000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr18:44628600-44635200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr18:44628600-44640000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr18:44628600-44640600	Weak transcription	Esophagus	oesophagus
39	chr18:44628600-44641400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr18:44629000-44637600	Weak transcription	NHDF-Ad	bronchial
41	chr18:44629200-44637800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
43	chr18:44629400-44634800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr18:44629400-44635200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr18:44629400-44642200	Strong transcription	Liver	Liver
46	chr18:44629400-44642400	Strong transcription	Primary T cells from cord blood	blood
47	chr18:44629600-44633000	Weak transcription	HSMMtube	muscle
48	chr18:44629600-44635000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr18:44629600-44640400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr18:44629800-44636600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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