Variant report

Variant	rs58175041
Chromosome Location	chr1:113541099-113541100
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	chr1:113493684..113495226-chr1:113539915..113542867,2	K562	blood:
2	chr1:113540112..113542991-chr1:113560118..113562958,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC16A1-4	chr1:113541027-113542835	ucscGeneNc_uc001edg_1

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

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	0.95[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	0.80[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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57514267	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57546902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60031820	0.95[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	0.97[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	0.97[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	0.92[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:13 , 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	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113510800-113541800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:113511200-113545800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:113511200-113546400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr1:113511200-113558000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:113511200-113558600	Weak transcription	NHDF-Ad	bronchial
6	chr1:113511200-113564000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:113514000-113541200	Weak transcription	K562	blood
8	chr1:113517800-113542800	Weak transcription	Dnd41	blood
9	chr1:113526400-113541600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:113526600-113564200	Weak transcription	Placenta	Placenta
11	chr1:113526800-113558600	Weak transcription	GM12878-XiMat	blood
12	chr1:113528200-113556600	Weak transcription	Small Intestine	intestine
13	chr1:113529000-113554400	Weak transcription	Lung	lung
14	chr1:113532200-113541600	Weak transcription	Thymus	Thymus
15	chr1:113533600-113555600	Weak transcription	Fetal Lung	lung
16	chr1:113534400-113541400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:113534400-113548400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:113535400-113544200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:113535600-113543400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:113535600-113549200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:113535600-113552200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:113535600-113557000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:113535800-113550600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:113535800-113564000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:113535800-113564000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:113535800-113564200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:113535800-113568800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:113537000-113543000	Enhancers	Fetal Heart	heart
29	chr1:113537200-113541200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:113537200-113554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:113537400-113541200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:113537400-113541200	Weak transcription	Osteobl	bone
33	chr1:113537400-113546000	Weak transcription	NHLF	lung
34	chr1:113537400-113550400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:113537400-113554200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:113537600-113541200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:113537600-113552800	Weak transcription	Fetal Thymus	thymus
38	chr1:113538200-113541400	Enhancers	Stomach Mucosa	stomach
39	chr1:113538400-113545200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:113538600-113542800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:113538600-113558600	Weak transcription	Spleen	Spleen
42	chr1:113538800-113546000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:113539200-113541200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:113539200-113541200	Genic enhancers	Fetal Stomach	stomach
45	chr1:113539200-113541600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:113539200-113547000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:113539400-113541600	Enhancers	Left Ventricle	heart
48	chr1:113539600-113564200	Weak transcription	Brain Germinal Matrix	brain
49	chr1:113539800-113541200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr1:113539800-113541400	Enhancers	Aorta	Aorta

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