Variant report

Variant	rs2109557
Chromosome Location	chr3:52448913-52448914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52445710..52451315-chr3:52451741..52455746,7	K562	blood:
2	chr3:52447983..52449593-chr3:52487471..52490265,2	K562	blood:

Variant related genes	Relation type
ENSG00000114854	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1011062	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1011064	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1035002	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1035003	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11706001	0.87[ASN][1000 genomes]
rs11707864	1.00[ASN][1000 genomes]
rs11707931	1.00[ASN][1000 genomes]
rs11709658	1.00[ASN][1000 genomes]
rs11716017	1.00[ASN][1000 genomes]
rs11721286	0.81[EUR][1000 genomes]
rs123598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123603	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060192	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13065677	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13071708	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13074649	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13075370	1.00[ASN][1000 genomes]
rs13076508	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089892	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091360	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093555	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13096571	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098856	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs164636	0.91[AMR][1000 genomes]
rs164637	0.91[AMR][1000 genomes]
rs17052068	1.00[ASN][1000 genomes]
rs2109558	0.81[EUR][1000 genomes]
rs2109559	0.81[EUR][1000 genomes]
rs2215466	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2335640	1.00[ASN][1000 genomes]
rs2335928	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2335929	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2878549	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181173	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34332947	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34355561	1.00[ASN][1000 genomes]
rs34385735	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34551211	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34628357	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762015	1.00[ASN][1000 genomes]
rs34827613	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34908451	1.00[ASN][1000 genomes]
rs35130772	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs35133416	1.00[ASN][1000 genomes]
rs352141	0.82[AMR][1000 genomes]
rs352144	0.86[AMR][1000 genomes]
rs353545	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35982798	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752819	1.00[ASN][1000 genomes]
rs3755810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3774409	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3796342	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs409803	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs419050	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419752	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312651	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4687541	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4687544	0.88[EUR][1000 genomes]
rs4687614	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4687617	0.81[EUR][1000 genomes]
rs4687618	0.88[EUR][1000 genomes]
rs4687619	0.88[EUR][1000 genomes]
rs4687621	0.88[EUR][1000 genomes]
rs498778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357549	1.00[ASN][1000 genomes]
rs575476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61150019	1.00[ASN][1000 genomes]
rs613519	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61734640	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414568	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6445484	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6445485	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6445486	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6445506	0.81[EUR][1000 genomes]
rs67248391	1.00[ASN][1000 genomes]
rs676034	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6763882	0.87[ASN][1000 genomes]
rs6771558	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6782162	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67834575	1.00[ASN][1000 genomes]
rs6784615	0.81[EUR][1000 genomes]
rs6787493	0.81[EUR][1000 genomes]
rs6794675	1.00[ASN][1000 genomes]
rs6795333	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810027	0.88[EUR][1000 genomes]
rs71297391	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297394	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297395	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297396	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	0.81[EUR][1000 genomes]
rs758800	0.88[EUR][1000 genomes]
rs758803	0.88[EUR][1000 genomes]
rs7620015	0.81[EUR][1000 genomes]
rs887514	0.81[EUR][1000 genomes]
rs929528	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs929529	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9846089	0.88[EUR][1000 genomes]
rs9847332	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9850471	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9855470	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9863753	0.81[EUR][1000 genomes]
rs9867823	0.88[EUR][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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52445600-52471600	Weak transcription	Gastric	stomach
2	chr3:52445800-52456800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52445800-52457200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:52445800-52457600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52446000-52450400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:52446200-52449600	Weak transcription	Pancreas	Pancrea
7	chr3:52446200-52452000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:52446200-52453600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:52446200-52454200	Weak transcription	Spleen	Spleen
10	chr3:52446200-52457400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:52446200-52463000	Weak transcription	Lung	lung
12	chr3:52446200-52465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:52446200-52467800	Weak transcription	Esophagus	oesophagus
14	chr3:52446400-52470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:52446600-52449600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:52446600-52450400	Weak transcription	Small Intestine	intestine
17	chr3:52446600-52450400	Weak transcription	HUVEC	blood vessel
18	chr3:52446600-52451200	Weak transcription	NH-A	brain
19	chr3:52446600-52451600	Weak transcription	A549	lung
20	chr3:52446600-52452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:52446600-52454200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:52446600-52454200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:52446600-52454200	Weak transcription	Placenta	Placenta
24	chr3:52446600-52454800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:52446600-52455000	Weak transcription	Fetal Stomach	stomach
26	chr3:52446600-52455800	Weak transcription	Fetal Brain Female	brain
27	chr3:52446600-52457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:52446800-52449600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:52446800-52451600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:52446800-52451600	Weak transcription	Fetal Brain Male	brain
31	chr3:52446800-52453200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:52446800-52455600	Weak transcription	Brain Substantia Nigra	brain
33	chr3:52446800-52456000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:52446800-52457200	Weak transcription	Primary B cells from cord blood	blood
35	chr3:52446800-52457200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:52446800-52457400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:52446800-52458200	Weak transcription	HepG2	liver
38	chr3:52446800-52460000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:52446800-52462400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:52446800-52463000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:52446800-52466000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:52447000-52449600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:52447000-52450400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:52447000-52451600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:52447000-52453200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:52447000-52454000	Weak transcription	Adipose Nuclei	Adipose
47	chr3:52447000-52456600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:52447000-52462800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:52447000-52464000	Weak transcription	Osteobl	bone
50	chr3:52447000-52470200	Weak transcription	Fetal Lung	lung

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