Variant report

Variant	rs7076219
Chromosome Location	chr10:91596920-91596921
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIF20B-2	chr10:91596744-91600600	NONHSAT015553

Extended variants
information (count: 68 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1125326	0.91[EUR][1000 genomes]
rs12240414	0.90[EUR][1000 genomes]
rs12244597	0.89[EUR][1000 genomes]
rs12252414	0.90[EUR][1000 genomes]
rs12263026	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12763878	0.81[EUR][1000 genomes]
rs12763984	0.91[EUR][1000 genomes]
rs12766364	0.91[EUR][1000 genomes]
rs12773439	0.91[EUR][1000 genomes]
rs12775585	0.81[EUR][1000 genomes]
rs1326198	0.89[EUR][1000 genomes]
rs1326199	0.92[EUR][1000 genomes]
rs17127746	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17127968	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128049	0.84[EUR][1000 genomes]
rs17385594	0.90[EUR][1000 genomes]
rs2148276	0.91[EUR][1000 genomes]
rs2181946	0.83[EUR][1000 genomes]
rs2182397	0.91[EUR][1000 genomes]
rs34395627	0.91[EUR][1000 genomes]
rs34407717	0.91[EUR][1000 genomes]
rs34498741	0.91[EUR][1000 genomes]
rs34498979	0.91[EUR][1000 genomes]
rs34548995	0.90[EUR][1000 genomes]
rs34833458	0.91[EUR][1000 genomes]
rs35305443	0.91[EUR][1000 genomes]
rs35494197	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35495765	0.91[EUR][1000 genomes]
rs35557724	0.91[EUR][1000 genomes]
rs35762262	0.81[EUR][1000 genomes]
rs35768372	0.91[EUR][1000 genomes]
rs36067049	0.91[EUR][1000 genomes]
rs36075457	0.91[EUR][1000 genomes]
rs3740040	0.92[EUR][1000 genomes]
rs3740042	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802651	0.92[EUR][1000 genomes]
rs55932503	0.90[EUR][1000 genomes]
rs55977662	0.91[EUR][1000 genomes]
rs56246606	0.91[EUR][1000 genomes]
rs56318801	0.91[EUR][1000 genomes]
rs57160906	0.91[EUR][1000 genomes]
rs57529292	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57585079	0.91[EUR][1000 genomes]
rs57603165	0.91[EUR][1000 genomes]
rs58929000	0.91[EUR][1000 genomes]
rs58933281	0.84[EUR][1000 genomes]
rs60634654	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60925336	0.91[EUR][1000 genomes]
rs61128077	0.91[EUR][1000 genomes]
rs61303211	0.91[EUR][1000 genomes]
rs61646033	0.82[EUR][1000 genomes]
rs61869791	0.82[EUR][1000 genomes]
rs61869800	0.82[EUR][1000 genomes]
rs68147789	0.93[EUR][1000 genomes]
rs7076194	0.93[EUR][1000 genomes]
rs7475158	0.91[EUR][1000 genomes]
rs7895272	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7895530	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7895851	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7895863	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7899499	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7908739	0.90[EUR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7076219	RP11-248C1.3	cis	Thyroid	GTEx
rs7076219	LINC00865	cis	Nerve Tibial	GTEx
rs7076219	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs7076219	LINC00865	cis	lung	GTEx
rs7076219	LINC00865	cis	Artery Aorta	GTEx
rs7076219	RP11-248C1.3	cis	Artery Tibial	GTEx
rs7076219	LINC00865	cis	Thyroid	GTEx
rs7076219	LINC00865	cis	Esophagus Muscularis	GTEx
rs7076219	LINC00865	cis	Adipose Subcutaneous	GTEx
rs7076219	RP11-248C1.3	cis	Artery Aorta	GTEx
rs7076219	LINC00865	cis	Artery Tibial	GTEx
rs7076219	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs7076219	RP11-248C1.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91596400-91597000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr10:91596400-91597000	Active TSS	Brain Cingulate Gyrus	brain
3	chr10:91596400-91598000	Active TSS	Fetal Intestine Large	intestine
4	chr10:91596600-91597000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
5	chr10:91596600-91597000	Active TSS	Primary hematopoietic stem cells	blood
6	chr10:91596600-91597000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr10:91596600-91597000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr10:91596600-91597000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
9	chr10:91596600-91597000	Active TSS	Brain Hippocampus Middle	brain
10	chr10:91596600-91597000	Flanking Active TSS	Fetal Thymus	thymus
11	chr10:91596600-91597000	Flanking Active TSS	Thymus	Thymus
12	chr10:91596600-91597000	Active TSS	HUVEC	blood vessel
13	chr10:91596600-91597200	Active TSS	Esophagus	oesophagus
14	chr10:91596600-91597200	Flanking Active TSS	Fetal Muscle Leg	muscle
15	chr10:91596600-91597200	Active TSS	Monocytes-CD14+_RO01746	blood
16	chr10:91596600-91597600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:91596600-91597600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr10:91596600-91597800	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr10:91596600-91597800	Active TSS	Stomach Mucosa	stomach
20	chr10:91596600-91597800	Active TSS	Stomach Smooth Muscle	stomach
21	chr10:91596600-91597800	Active TSS	NHDF-Ad	bronchial
22	chr10:91596600-91598000	Active TSS	Primary T cells from cord blood	blood
23	chr10:91596600-91598000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr10:91596600-91598000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr10:91596600-91598000	Active TSS	Lung	lung
26	chr10:91596600-91598200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:91596600-91598200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:91596600-91598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:91596600-91598200	Active TSS	Brain Substantia Nigra	brain
31	chr10:91596600-91598200	Active TSS	Fetal Brain Female	brain
32	chr10:91596600-91598200	Active TSS	Fetal Intestine Small	intestine
33	chr10:91596600-91598400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:91596600-91598400	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr10:91596600-91598400	Active TSS	Rectal Smooth Muscle	rectum
36	chr10:91596600-91598600	Active TSS	Brain Anterior Caudate	brain
37	chr10:91596600-91598600	Active TSS	Duodenum Mucosa	Duodenum
38	chr10:91596800-91597000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr10:91596800-91597000	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr10:91596800-91597000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
41	chr10:91596800-91597000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr10:91596800-91597000	Active TSS	Liver	Liver
43	chr10:91596800-91597000	Active TSS	Psoas Muscle	Psoas
44	chr10:91596800-91597000	Enhancers	Spleen	Spleen
45	chr10:91596800-91597000	Enhancers	HMEC	breast
46	chr10:91596800-91597000	Active TSS	NH-A	brain
47	chr10:91596800-91597200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr10:91596800-91597200	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr10:91596800-91597200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
50	chr10:91596800-91597200	Flanking Active TSS	Adipose Nuclei	Adipose

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