Variant report

Variant	rs57514267
Chromosome Location	chr1:113554902-113554903
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	chr1:113549141..113551192-chr1:113554821..113556878,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC16A1-2	chr1:113554309-113556461	ENSG00000238198

Variant related genes	Relation type
ENSG00000236066	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10158316	1.00[EUR][1000 genomes]
rs12059435	1.00[EUR][1000 genomes]
rs12067118	1.00[EUR][1000 genomes]
rs12070103	1.00[EUR][1000 genomes]
rs12070165	1.00[EUR][1000 genomes]
rs17030801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17030825	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17030972	1.00[EUR][1000 genomes]
rs17031107	1.00[EUR][1000 genomes]
rs3866218	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3892517	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41510545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55879014	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56037773	1.00[EUR][1000 genomes]
rs57546902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58175041	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60031820	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60103137	1.00[EUR][1000 genomes]
rs60860858	1.00[EUR][1000 genomes]
rs61134101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6657154	1.00[EUR][1000 genomes]
rs6678201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6694556	1.00[EUR][1000 genomes]
rs6697225	1.00[EUR][1000 genomes]
rs72982471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72984355	1.00[EUR][1000 genomes]
rs72986328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72986329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72986335	1.00[EUR][1000 genomes]
rs72986336	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72986345	1.00[EUR][1000 genomes]
rs73000304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73000323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73000328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7531239	1.00[EUR][1000 genomes]
rs7534668	1.00[EUR][1000 genomes]
rs7539797	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7540353	1.00[AMR][1000 genomes]
rs7541153	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9308259	1.00[EUR][1000 genomes]
rs9429498	1.00[EUR][1000 genomes]
rs9429499	1.00[EUR][1000 genomes]
rs9429502	1.00[EUR][1000 genomes]
rs9429699	1.00[EUR][1000 genomes]
rs9429703	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
10	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113511200-113558000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr1:113511200-113558600	Weak transcription	NHDF-Ad	bronchial
3	chr1:113511200-113564000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:113526600-113564200	Weak transcription	Placenta	Placenta
5	chr1:113526800-113558600	Weak transcription	GM12878-XiMat	blood
6	chr1:113528200-113556600	Weak transcription	Small Intestine	intestine
7	chr1:113533600-113555600	Weak transcription	Fetal Lung	lung
8	chr1:113535600-113557000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:113535800-113564000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:113535800-113564000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:113535800-113564200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:113535800-113568800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:113538600-113558600	Weak transcription	Spleen	Spleen
14	chr1:113539600-113564200	Weak transcription	Brain Germinal Matrix	brain
15	chr1:113541000-113573800	Weak transcription	Right Ventricle	heart
16	chr1:113541600-113555600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:113541600-113564200	Weak transcription	Osteobl	bone
18	chr1:113541800-113564000	Weak transcription	K562	blood
19	chr1:113542000-113558400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:113542000-113564000	Weak transcription	Hela-S3	cervix
21	chr1:113542800-113559200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:113543000-113555000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:113543000-113555200	Weak transcription	Fetal Heart	heart
24	chr1:113543000-113555800	Weak transcription	Stomach Mucosa	stomach
25	chr1:113543200-113574400	Weak transcription	HSMM	muscle
26	chr1:113543400-113555200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:113543400-113556600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:113547200-113555800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:113547400-113555200	Weak transcription	Fetal Intestine Small	intestine
30	chr1:113547400-113564000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:113547800-113555200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:113547800-113556600	Weak transcription	Fetal Intestine Large	intestine
33	chr1:113550800-113563400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:113551000-113564000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:113551200-113555000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:113551200-113555200	Weak transcription	Primary T cells from cord blood	blood
37	chr1:113551200-113555200	Weak transcription	HepG2	liver
38	chr1:113551200-113556000	Weak transcription	Brain Anterior Caudate	brain
39	chr1:113551200-113561800	Weak transcription	Dnd41	blood
40	chr1:113551200-113563200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:113551200-113564000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:113551200-113564000	Weak transcription	HMEC	breast
43	chr1:113551200-113564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:113551200-113564400	Weak transcription	Adipose Nuclei	Adipose
45	chr1:113551200-113569800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:113551200-113569800	Weak transcription	Left Ventricle	heart
47	chr1:113551400-113555000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:113551400-113555800	Weak transcription	Liver	Liver
49	chr1:113551400-113558000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:113552600-113559200	Weak transcription	Fetal Muscle Trunk	muscle

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