Variant report

Variant	rs3740042
Chromosome Location	chr10:91597919-91597920
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: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: 69 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1125326	0.89[EUR][1000 genomes]
rs12240414	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs12244597	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs12252414	0.88[EUR][1000 genomes]
rs12263026	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12265484	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs12763984	0.89[EUR][1000 genomes]
rs12766364	0.89[EUR][1000 genomes]
rs12773439	0.89[EUR][1000 genomes]
rs1326198	0.89[EUR][1000 genomes]
rs1326199	0.92[EUR][1000 genomes]
rs17127746	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17127968	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128049	0.82[EUR][1000 genomes]
rs17385594	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2148276	0.89[EUR][1000 genomes]
rs2181946	0.83[EUR][1000 genomes]
rs2182397	0.89[EUR][1000 genomes]
rs34395627	0.89[EUR][1000 genomes]
rs34407717	0.89[EUR][1000 genomes]
rs34498741	0.89[EUR][1000 genomes]
rs34498979	0.89[EUR][1000 genomes]
rs34548995	0.88[EUR][1000 genomes]
rs34833458	0.89[EUR][1000 genomes]
rs35305443	0.89[EUR][1000 genomes]
rs35494197	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35495765	0.89[EUR][1000 genomes]
rs35557724	0.89[EUR][1000 genomes]
rs35768372	0.89[EUR][1000 genomes]
rs36067049	0.89[EUR][1000 genomes]
rs36075457	0.89[EUR][1000 genomes]
rs3740040	0.92[EUR][1000 genomes]
rs3802651	0.92[EUR][1000 genomes]
rs55932503	0.88[EUR][1000 genomes]
rs55977662	0.89[EUR][1000 genomes]
rs56246606	0.89[EUR][1000 genomes]
rs56318801	0.89[EUR][1000 genomes]
rs57160906	0.89[EUR][1000 genomes]
rs57529292	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57585079	0.89[EUR][1000 genomes]
rs57603165	0.89[EUR][1000 genomes]
rs58929000	0.89[EUR][1000 genomes]
rs58933281	0.82[EUR][1000 genomes]
rs60634654	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60925336	0.89[EUR][1000 genomes]
rs61128077	0.89[EUR][1000 genomes]
rs61303211	0.89[EUR][1000 genomes]
rs61646033	0.81[EUR][1000 genomes]
rs61869791	0.81[EUR][1000 genomes]
rs61869800	0.81[EUR][1000 genomes]
rs6583662	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs68147789	0.91[EUR][1000 genomes]
rs7076194	0.91[EUR][1000 genomes]
rs7076219	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7083051	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7475158	0.89[EUR][1000 genomes]
rs7895272	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7895530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7895851	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7895863	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7899499	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7908739	0.88[EUR][1000 genomes]
rs7918018	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3740042	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs3740042	LINC00865	cis	Thyroid	GTEx
rs3740042	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs3740042	RP11-248C1.3	cis	Artery Tibial	GTEx
rs3740042	RP11-248C1.3	cis	Thyroid	GTEx
rs3740042	RP11-248C1.3	cis	Artery Aorta	GTEx
rs3740042	RP11-248C1.3	cis	Esophagus Muscularis	GTEx
rs3740042	LINC00865	cis	Artery Tibial	GTEx
rs3740042	LINC00865	cis	Artery Aorta	GTEx
rs3740042	LINC00865	cis	lung	GTEx
rs3740042	LINC00865	cis	Esophagus Muscularis	GTEx
rs3740042	LINC00865	cis	Adipose Subcutaneous	GTEx
rs3740042	LINC00865	cis	Nerve Tibial	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91596400-91598000	Active TSS	Fetal Intestine Large	intestine
2	chr10:91596600-91598000	Active TSS	Primary T cells from cord blood	blood
3	chr10:91596600-91598000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr10:91596600-91598000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:91596600-91598000	Active TSS	Lung	lung
6	chr10:91596600-91598200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:91596600-91598200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:91596600-91598200	Active TSS	Brain Substantia Nigra	brain
11	chr10:91596600-91598200	Active TSS	Fetal Brain Female	brain
12	chr10:91596600-91598200	Active TSS	Fetal Intestine Small	intestine
13	chr10:91596600-91598400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:91596600-91598400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr10:91596600-91598400	Active TSS	Rectal Smooth Muscle	rectum
16	chr10:91596600-91598600	Active TSS	Brain Anterior Caudate	brain
17	chr10:91596600-91598600	Active TSS	Duodenum Mucosa	Duodenum
18	chr10:91596800-91598000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr10:91596800-91598000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr10:91596800-91598000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:91596800-91598000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr10:91596800-91598000	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr10:91596800-91598000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr10:91596800-91598000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:91596800-91598000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr10:91596800-91598000	Active TSS	Fetal Lung	lung
27	chr10:91596800-91598000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr10:91596800-91598000	Flanking Active TSS	Placenta	Placenta
29	chr10:91596800-91598000	Active TSS	Gastric	stomach
30	chr10:91596800-91598000	Active TSS	Left Ventricle	heart
31	chr10:91596800-91598000	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr10:91596800-91598000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
33	chr10:91596800-91598000	Active TSS	Osteobl	bone
34	chr10:91596800-91598200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:91596800-91598200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
36	chr10:91596800-91598200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr10:91596800-91598200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
38	chr10:91596800-91598200	Active TSS	Aorta	Aorta
39	chr10:91596800-91598200	Active TSS	Brain Angular Gyrus	brain
40	chr10:91596800-91598200	Active TSS	Colon Smooth Muscle	Colon
41	chr10:91596800-91598200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr10:91596800-91598200	Active TSS	Ovary	ovary
43	chr10:91596800-91598200	Active TSS	Right Atrium	heart
44	chr10:91596800-91598200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
45	chr10:91596800-91598400	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr10:91596800-91598800	Active TSS	Fetal Kidney	kidney
47	chr10:91597000-91598000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:91597000-91598000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr10:91597000-91598000	Bivalent/Poised TSS	Psoas Muscle	Psoas
50	chr10:91597000-91598200	Active TSS	HUES6 Cell Line	embryonic stem cell

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