Variant report

Variant	rs58933281
Chromosome Location	chr10:91598174-91598175
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91596297..91598343-chr10:91607270..91608932,2	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIF20B-2	chr10:91596975-91600618	ENSG00000232229
2	lnc-KIF20B-2	chr10:91596975-91600618	ENSG00000232229
3	lnc-KIF20B-2	chr10:91596975-91600618	NONHSAT015546
4	lnc-KIF20B-2	chr10:91596975-91599568	NONHSAT015550
5	lnc-KIF20B-2	chr10:91596744-91600600	NONHSAT015553
6	lnc-PANK1-6	chr10:91597369-91599091	NONHSAT015554

No data

Extended variants
information (count: 81 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1125326	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11593486	0.81[ASN][1000 genomes]
rs12240414	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12244597	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12252414	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12263026	0.86[EUR][1000 genomes]
rs12763878	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12763984	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12766364	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12770938	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773439	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12775585	0.97[EUR][1000 genomes]
rs1326198	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326199	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408582	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127746	0.84[EUR][1000 genomes]
rs17127968	0.84[EUR][1000 genomes]
rs17128049	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128178	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385594	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998643	0.81[ASN][1000 genomes]
rs2148276	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181946	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182397	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34395627	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34407717	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34498741	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34498979	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34548995	0.87[EUR][1000 genomes]
rs34768430	0.81[ASN][1000 genomes]
rs34833458	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35305443	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35494197	0.84[EUR][1000 genomes]
rs35495765	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35557724	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35569149	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35606974	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35762262	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35768372	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36067049	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36075457	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3740040	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740042	0.82[EUR][1000 genomes]
rs3802651	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932503	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55977662	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56246606	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56318801	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57160906	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57529292	0.81[EUR][1000 genomes]
rs57585079	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57603165	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58250931	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58929000	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60634654	0.83[EUR][1000 genomes]
rs60925336	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61128077	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61303211	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61646033	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61869791	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61869800	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61869806	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68147789	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7076194	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7076219	0.84[EUR][1000 genomes]
rs7098084	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7475158	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7895272	0.84[EUR][1000 genomes]
rs7895851	0.84[EUR][1000 genomes]
rs7895863	0.84[EUR][1000 genomes]
rs7899499	0.84[EUR][1000 genomes]
rs7908739	0.87[EUR][1000 genomes]
rs7908779	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908953	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7912390	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046241	chr10:91478562-91614437	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv869080	chr10:91498641-91712834	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1036581	chr10:91526705-91691536	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv949678	chr10:91589048-92016474	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs58933281	LINC00865	cis	Artery Aorta	GTEx
rs58933281	LINC00865	cis	Artery Tibial	GTEx
rs58933281	LINC00865	cis	Nerve Tibial	GTEx
rs58933281	LINC00865	cis	Adipose Subcutaneous	GTEx
rs58933281	LINC00865	cis	Esophagus Muscularis	GTEx
rs58933281	RP11-248C1.3	cis	Esophagus Muscularis	GTEx
rs58933281	RP11-248C1.3	cis	lung	GTEx
rs58933281	LINC00865	cis	Skin Sun Exposed Lower leg	GTEx
rs58933281	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs58933281	RP11-248C1.3	cis	Artery Aorta	GTEx
rs58933281	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs58933281	RP11-248C1.3	cis	Thyroid	GTEx
rs58933281	LINC00865	cis	Heart Left Ventricle	GTEx
rs58933281	LINC00865	cis	Thyroid	GTEx
rs58933281	RP11-248C1.3	cis	Artery Tibial	GTEx
rs58933281	LINC00865	cis	lung	GTEx
rs58933281	LINC00865	cis	Whole Blood	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91596600-91598200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:91596600-91598200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:91596600-91598200	Active TSS	Brain Substantia Nigra	brain
6	chr10:91596600-91598200	Active TSS	Fetal Brain Female	brain
7	chr10:91596600-91598200	Active TSS	Fetal Intestine Small	intestine
8	chr10:91596600-91598400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:91596600-91598400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr10:91596600-91598400	Active TSS	Rectal Smooth Muscle	rectum
11	chr10:91596600-91598600	Active TSS	Brain Anterior Caudate	brain
12	chr10:91596600-91598600	Active TSS	Duodenum Mucosa	Duodenum
13	chr10:91596800-91598200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:91596800-91598200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
15	chr10:91596800-91598200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:91596800-91598200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:91596800-91598200	Active TSS	Aorta	Aorta
18	chr10:91596800-91598200	Active TSS	Brain Angular Gyrus	brain
19	chr10:91596800-91598200	Active TSS	Colon Smooth Muscle	Colon
20	chr10:91596800-91598200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
21	chr10:91596800-91598200	Active TSS	Ovary	ovary
22	chr10:91596800-91598200	Active TSS	Right Atrium	heart
23	chr10:91596800-91598200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
24	chr10:91596800-91598400	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr10:91596800-91598800	Active TSS	Fetal Kidney	kidney
26	chr10:91597000-91598200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr10:91597000-91598200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr10:91597000-91598400	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr10:91597000-91598400	Active TSS	Thymus	Thymus
30	chr10:91597000-91598800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
31	chr10:91597200-91598200	Active TSS	Right Ventricle	heart
32	chr10:91597200-91598400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
33	chr10:91597200-91598400	Active TSS	Colonic Mucosa	Colon
34	chr10:91597400-91598200	Active TSS	H1 Cell Line	embryonic stem cell
35	chr10:91597400-91598200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:91597400-91598200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:91597400-91598400	Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr10:91597400-91598400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
39	chr10:91597600-91598200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr10:91597600-91598200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
41	chr10:91597600-91598200	Flanking Active TSS	Esophagus	oesophagus
42	chr10:91597600-91598200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
43	chr10:91597600-91598400	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr10:91597600-91598400	Flanking Active TSS	Fetal Thymus	thymus
45	chr10:91597800-91598200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr10:91597800-91598200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr10:91597800-91598200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
48	chr10:91597800-91598200	Enhancers	Fetal Heart	heart
49	chr10:91597800-91598200	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr10:91597800-91598200	Enhancers	Spleen	Spleen

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