Variant report

Variant	rs3740040
Chromosome Location	chr10:91597426-91597427
allele	C/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:2)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:2 , 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:
2	chr10:91596270..91598135-chr10:91628294..91631129,2	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: 87 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1125326	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11593486	0.81[ASN][1000 genomes]
rs11814174	0.82[CHB][hapmap]
rs12240414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12244597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12252414	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12263026	0.96[EUR][1000 genomes]
rs12265484	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs12763878	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12763984	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12766364	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12770938	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12773439	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12775585	0.87[EUR][1000 genomes]
rs1326198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408582	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17127746	0.92[EUR][1000 genomes]
rs17127968	0.94[EUR][1000 genomes]
rs17128049	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128178	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17385594	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998643	0.81[ASN][1000 genomes]
rs2148276	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181946	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182397	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34395627	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34407717	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34498741	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34498979	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34548995	0.96[EUR][1000 genomes]
rs34768430	0.81[ASN][1000 genomes]
rs34833458	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35305443	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35494197	0.92[EUR][1000 genomes]
rs35495765	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35557724	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35569149	0.93[ASN][1000 genomes]
rs35606974	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35762262	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35768372	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36067049	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36075457	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3740042	0.92[EUR][1000 genomes]
rs3802651	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932503	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55977662	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56246606	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56318801	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57160906	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57529292	0.89[EUR][1000 genomes]
rs57585079	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57603165	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58250931	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58929000	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58933281	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60634654	0.93[EUR][1000 genomes]
rs60925336	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61128077	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61303211	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61646033	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61869791	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61869800	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61869806	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6583662	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs68147789	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7076194	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7076219	0.92[EUR][1000 genomes]
rs7083051	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs7098084	1.00[ASN][1000 genomes]
rs7475158	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7895272	0.92[EUR][1000 genomes]
rs7895530	0.84[CEU][hapmap]
rs7895851	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs7895863	0.91[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs7899499	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7908739	0.96[EUR][1000 genomes]
rs7908779	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7908953	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7912390	1.00[ASN][1000 genomes]
rs7918018	1.00[CEU][hapmap]

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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs3740040	LINC00865	cis	Whole Blood	GTEx
rs3740040	RP11-248C1.3	cis	Thyroid	GTEx
rs3740040	RP11-248C1.3	cis	Artery Tibial	GTEx
rs3740040	RP11-248C1.3	cis	Esophagus Muscularis	GTEx
rs3740040	KIF20B	cis	cerebellum	SCAN
rs3740040	LINC00865	cis	Thyroid	GTEx
rs3740040	LINC00865	cis	Heart Left Ventricle	GTEx
rs3740040	LINC00865	cis	Artery Aorta	GTEx
rs3740040	LINC00865	cis	lung	GTEx
rs3740040	LIPJ	cis	parietal	SCAN
rs3740040	LINC00865	cis	Nerve Tibial	GTEx
rs3740040	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs3740040	RP11-248C1.3	cis	Artery Aorta	GTEx
rs3740040	SNCG	cis	parietal	SCAN
rs3740040	RP11-248C1.3	cis	lung	GTEx
rs3740040	LINC00865	cis	Adipose Subcutaneous	GTEx
rs3740040	LINC00865	cis	Esophagus Muscularis	GTEx
rs3740040	LINC00865	cis	Artery Tibial	GTEx
rs3740040	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs3740040	LINC00865	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:105 , 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	chr10:91596600-91597600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:91596600-91597600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr10:91596600-91597800	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr10:91596600-91597800	Active TSS	Stomach Mucosa	stomach
6	chr10:91596600-91597800	Active TSS	Stomach Smooth Muscle	stomach
7	chr10:91596600-91597800	Active TSS	NHDF-Ad	bronchial
8	chr10:91596600-91598000	Active TSS	Primary T cells from cord blood	blood
9	chr10:91596600-91598000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr10:91596600-91598000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:91596600-91598000	Active TSS	Lung	lung
12	chr10:91596600-91598200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr10:91596600-91598200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:91596600-91598200	Active TSS	Brain Substantia Nigra	brain
17	chr10:91596600-91598200	Active TSS	Fetal Brain Female	brain
18	chr10:91596600-91598200	Active TSS	Fetal Intestine Small	intestine
19	chr10:91596600-91598400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:91596600-91598400	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr10:91596600-91598400	Active TSS	Rectal Smooth Muscle	rectum
22	chr10:91596600-91598600	Active TSS	Brain Anterior Caudate	brain
23	chr10:91596600-91598600	Active TSS	Duodenum Mucosa	Duodenum
24	chr10:91596800-91597600	Active TSS	Fetal Heart	heart
25	chr10:91596800-91597600	Active TSS	Placenta Amnion	Placenta Amnion
26	chr10:91596800-91597600	Active TSS	K562	blood
27	chr10:91596800-91597600	Active TSS	NHLF	lung
28	chr10:91596800-91597800	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr10:91596800-91597800	Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr10:91596800-91597800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr10:91596800-91597800	Active TSS	Fetal Brain Male	brain
32	chr10:91596800-91597800	Active TSS	Small Intestine	intestine
33	chr10:91596800-91597800	Flanking Active TSS	NHEK	skin
34	chr10:91596800-91598000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr10:91596800-91598000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:91596800-91598000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr10:91596800-91598000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr10:91596800-91598000	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr10:91596800-91598000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr10:91596800-91598000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:91596800-91598000	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr10:91596800-91598000	Active TSS	Fetal Lung	lung
43	chr10:91596800-91598000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
44	chr10:91596800-91598000	Flanking Active TSS	Placenta	Placenta
45	chr10:91596800-91598000	Active TSS	Gastric	stomach
46	chr10:91596800-91598000	Active TSS	Left Ventricle	heart
47	chr10:91596800-91598000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr10:91596800-91598000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
49	chr10:91596800-91598000	Active TSS	Osteobl	bone
50	chr10:91596800-91598200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung

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