Variant report

Variant	rs56003577
Chromosome Location	chr18:44632538-44632539
allele	A/T
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: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs55633240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55650860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55682632	1.00[AFR][1000 genomes]
rs55754830	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55840418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55877804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55916944	1.00[AFR][1000 genomes]
rs55929919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56009869	1.00[AFR][1000 genomes]
rs56101223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56109213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56119924	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56132373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56142565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56163470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56169983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56272937	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56297904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56299848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61743415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61743594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72903234	1.00[EUR][1000 genomes]
rs72903239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903245	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903247	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72903295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72905460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72907111	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907120	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs72907122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907125	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907137	1.00[AFR][1000 genomes]
rs72907140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72907220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72907225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72907230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72907240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72909104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72909181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72909200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72909204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72909212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72909229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72909252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72909254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72909289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72911116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72911123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72911203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72911205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72911207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72913049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72913052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72913066	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72913075	0.94[EUR][1000 genomes]
rs72913087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72913164	1.00[AFR][1000 genomes]
rs72913166	1.00[AFR][1000 genomes]
rs72913186	1.00[AFR][1000 genomes]
rs72913187	1.00[AFR][1000 genomes]
rs72914811	1.00[AFR][1000 genomes]
rs72914843	1.00[AFR][1000 genomes]
rs72915064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72915071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72917106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72917111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72917116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72917122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72917167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72917200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72917202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919221	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72919226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919241	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72919260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919289	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72919296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72921303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72921305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72921319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[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	chr18:44612600-44632600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr18:44613800-44638200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr18:44617200-44635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:44620600-44635000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:44620800-44675400	Weak transcription	A549	lung
11	chr18:44621200-44634800	Weak transcription	Pancreas	Pancrea
12	chr18:44621400-44638600	Weak transcription	Colonic Mucosa	Colon
13	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
14	chr18:44622000-44633200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr18:44622400-44633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr18:44623000-44637400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr18:44623200-44635200	Weak transcription	HepG2	liver
18	chr18:44623800-44635000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr18:44624200-44634800	Weak transcription	Gastric	stomach
20	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
21	chr18:44624400-44637400	Weak transcription	HMEC	breast
22	chr18:44624400-44640600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr18:44624600-44635000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr18:44626800-44632600	Weak transcription	NH-A	brain
26	chr18:44626800-44633000	Weak transcription	Placenta	Placenta
27	chr18:44626800-44634600	Weak transcription	NHEK	skin
28	chr18:44626800-44637400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr18:44627000-44632600	Weak transcription	Fetal Brain Female	brain
30	chr18:44627000-44633600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr18:44627000-44635000	Weak transcription	Brain Germinal Matrix	brain
32	chr18:44627000-44636600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr18:44627200-44632600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr18:44627200-44632600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr18:44627200-44635200	Weak transcription	Fetal Intestine Small	intestine
36	chr18:44627200-44638000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr18:44627600-44633600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr18:44628200-44640200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr18:44628400-44637800	Weak transcription	GM12878-XiMat	blood
40	chr18:44628600-44633000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr18:44628600-44635200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr18:44628600-44640000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr18:44628600-44640600	Weak transcription	Esophagus	oesophagus
44	chr18:44628600-44641400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr18:44629000-44637600	Weak transcription	NHDF-Ad	bronchial
46	chr18:44629200-44637800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
48	chr18:44629400-44634800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr18:44629400-44635200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr18:44629400-44642200	Strong transcription	Liver	Liver

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