Variant report

Variant	rs61869800
Chromosome Location	chr10:91597108-91597109
allele	A/G
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:3)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:91590785..91592404-chr10:91594759..91597371,2	MCF-7	breast:
2	chr10:91596297..91598343-chr10:91607270..91608932,2	MCF-7	breast:
3	chr10:91596270..91598135-chr10:91628294..91631129,2	MCF-7	breast:

(count:5 , 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

No data

Extended variants
information (count: 77 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1125326	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12240414	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12244597	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12252414	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12263026	0.84[EUR][1000 genomes]
rs12763878	0.95[ASN][1000 genomes]
rs12763984	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12766364	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12770938	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12773439	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12775585	0.99[EUR][1000 genomes]
rs1326198	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1326199	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408582	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17127746	0.82[EUR][1000 genomes]
rs17127968	0.86[EUR][1000 genomes]
rs17128049	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17128178	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17385594	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2148276	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2181946	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2182397	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34395627	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34407717	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34498741	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34498979	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34548995	0.89[EUR][1000 genomes]
rs34833458	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35305443	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35494197	0.82[EUR][1000 genomes]
rs35495765	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35557724	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35569149	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35606974	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35762262	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35768372	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36067049	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36075457	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740040	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3740042	0.81[EUR][1000 genomes]
rs3802651	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55932503	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55977662	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56246606	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56318801	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57160906	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57585079	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57603165	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58250931	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58929000	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58933281	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60634654	0.84[EUR][1000 genomes]
rs60925336	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61128077	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61303211	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61646033	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61869791	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61869806	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68147789	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7076194	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7076219	0.82[EUR][1000 genomes]
rs7098084	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7475158	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7895272	0.82[EUR][1000 genomes]
rs7895851	0.82[EUR][1000 genomes]
rs7895863	0.82[EUR][1000 genomes]
rs7899499	0.82[EUR][1000 genomes]
rs7908739	0.89[EUR][1000 genomes]
rs7908779	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7908953	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7912390	0.84[EUR][1000 genomes];0.93[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs61869800	RP11-248C1.3	cis	Esophagus Muscularis	GTEx
rs61869800	RP11-248C1.3	cis	lung	GTEx
rs61869800	LINC00865	cis	Skin Sun Exposed Lower leg	GTEx
rs61869800	LINC00865	cis	Whole Blood	GTEx
rs61869800	LINC00865	cis	Artery Aorta	GTEx
rs61869800	RP11-248C1.3	cis	Artery Tibial	GTEx
rs61869800	LINC00865	cis	Nerve Tibial	GTEx
rs61869800	LINC00865	cis	Esophagus Muscularis	GTEx
rs61869800	LINC00865	cis	lung	GTEx
rs61869800	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs61869800	LINC00865	cis	Adipose Subcutaneous	GTEx
rs61869800	RP11-248C1.3	cis	Thyroid	GTEx
rs61869800	RP11-248C1.3	cis	Artery Aorta	GTEx
rs61869800	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs61869800	LINC00865	cis	Thyroid	GTEx
rs61869800	LINC00865	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91596400-91598000	Active TSS	Fetal Intestine Large	intestine
2	chr10:91596600-91597200	Active TSS	Esophagus	oesophagus
3	chr10:91596600-91597200	Flanking Active TSS	Fetal Muscle Leg	muscle
4	chr10:91596600-91597200	Active TSS	Monocytes-CD14+_RO01746	blood
5	chr10:91596600-91597600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:91596600-91597600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr10:91596600-91597800	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr10:91596600-91597800	Active TSS	Stomach Mucosa	stomach
9	chr10:91596600-91597800	Active TSS	Stomach Smooth Muscle	stomach
10	chr10:91596600-91597800	Active TSS	NHDF-Ad	bronchial
11	chr10:91596600-91598000	Active TSS	Primary T cells from cord blood	blood
12	chr10:91596600-91598000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr10:91596600-91598000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:91596600-91598000	Active TSS	Lung	lung
15	chr10:91596600-91598200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr10:91596600-91598200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:91596600-91598200	Active TSS	Brain Substantia Nigra	brain
20	chr10:91596600-91598200	Active TSS	Fetal Brain Female	brain
21	chr10:91596600-91598200	Active TSS	Fetal Intestine Small	intestine
22	chr10:91596600-91598400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:91596600-91598400	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr10:91596600-91598400	Active TSS	Rectal Smooth Muscle	rectum
25	chr10:91596600-91598600	Active TSS	Brain Anterior Caudate	brain
26	chr10:91596600-91598600	Active TSS	Duodenum Mucosa	Duodenum
27	chr10:91596800-91597200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:91596800-91597200	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr10:91596800-91597200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
30	chr10:91596800-91597200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr10:91596800-91597200	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr10:91596800-91597200	Flanking Active TSS	Colonic Mucosa	Colon
33	chr10:91596800-91597200	Flanking Active TSS	Pancreas	Pancrea
34	chr10:91596800-91597200	Flanking Active TSS	Right Ventricle	heart
35	chr10:91596800-91597400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:91596800-91597400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:91596800-91597400	Active TSS	Fetal Stomach	stomach
38	chr10:91596800-91597600	Active TSS	Fetal Heart	heart
39	chr10:91596800-91597600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr10:91596800-91597600	Active TSS	K562	blood
41	chr10:91596800-91597600	Active TSS	NHLF	lung
42	chr10:91596800-91597800	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr10:91596800-91597800	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr10:91596800-91597800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:91596800-91597800	Active TSS	Fetal Brain Male	brain
46	chr10:91596800-91597800	Active TSS	Small Intestine	intestine
47	chr10:91596800-91597800	Flanking Active TSS	NHEK	skin
48	chr10:91596800-91598000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr10:91596800-91598000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr10:91596800-91598000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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