Variant report

Variant	rs2296600
Chromosome Location	chr10:90770439-90770440
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAMBPL1-1	chr10:90770296-90770709	NONHSAT015491

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10887882	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10887883	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12775232	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1324551	0.90[JPT][hapmap]
rs1571011	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1571013	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1571019	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800682	0.91[JPT][hapmap]
rs1810763	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1926191	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1926192	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1926193	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1926194	0.86[AFR][1000 genomes]
rs1926195	0.90[JPT][hapmap]
rs1926196	0.91[JPT][hapmap]
rs1977389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2031610	0.82[CEU][hapmap]
rs2031612	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147420	0.85[AFR][1000 genomes]
rs2148286	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2148287	0.86[AFR][1000 genomes]
rs2182408	0.84[AFR][1000 genomes]
rs2296603	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2862833	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35150762	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3740286	0.95[JPT][hapmap]
rs3752985	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3752986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781202	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3824730	0.95[JPT][hapmap]
rs4406737	0.85[AFR][1000 genomes]
rs4406738	0.82[AFR][1000 genomes]
rs4934434	0.95[JPT][hapmap]
rs6586163	0.91[JPT][hapmap]
rs6586164	0.91[JPT][hapmap]
rs6586165	0.91[JPT][hapmap]
rs6586167	0.91[JPT][hapmap]
rs7069750	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7089558	0.85[ASN][1000 genomes]
rs7095466	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7096473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7097572	0.91[JPT][hapmap]
rs7901656	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7910435	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910825	0.85[JPT][hapmap]
rs7911226	0.84[ASN][1000 genomes]
rs7911752	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs913043	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9658741	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9658742	0.83[ASN][1000 genomes]
rs982764	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv551841	chr10:90759724-90775756	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2296600	FAS	cis	Muscle Skeletal	GTEx
rs2296600	FAS	cis	Adipose Subcutaneous	GTEx
rs2296600	ACTA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90752000-90770800	Weak transcription	Esophagus	oesophagus
2	chr10:90752800-90773400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr10:90754000-90779400	Weak transcription	HepG2	liver
4	chr10:90754000-90789600	Weak transcription	A549	lung
5	chr10:90755600-90771400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:90755600-90776000	Weak transcription	Left Ventricle	heart
7	chr10:90755600-90776200	Weak transcription	Pancreas	Pancrea
8	chr10:90756200-90781800	Weak transcription	Stomach Mucosa	stomach
9	chr10:90757000-90770800	Weak transcription	Primary B cells from cord blood	blood
10	chr10:90760400-90780400	Weak transcription	Brain Angular Gyrus	brain
11	chr10:90761600-90779000	Weak transcription	Dnd41	blood
12	chr10:90761600-90779400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:90761800-90770800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr10:90761800-90773200	Weak transcription	Thymus	Thymus
15	chr10:90761800-90774200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:90761800-90776200	Weak transcription	Right Ventricle	heart
17	chr10:90761800-90779600	Weak transcription	HSMMtube	muscle
18	chr10:90761800-90779800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:90761800-90783800	Weak transcription	Gastric	stomach
20	chr10:90761800-90786200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr10:90762000-90770600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:90762000-90775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr10:90762200-90771200	Weak transcription	Brain Anterior Caudate	brain
24	chr10:90762200-90771400	Weak transcription	Fetal Stomach	stomach
25	chr10:90762400-90775400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr10:90762400-90785800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:90762600-90773600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr10:90762600-90777400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr10:90762600-90779400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr10:90762600-90780400	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:90762600-90786000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr10:90762800-90770800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr10:90762800-90773400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:90762800-90778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:90762800-90781000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:90762800-90782000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr10:90763000-90779600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr10:90763400-90777600	Strong transcription	NHDF-Ad	bronchial
39	chr10:90763600-90773600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:90763600-90780800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:90764000-90770800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr10:90766000-90780400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr10:90766200-90785600	Strong transcription	GM12878-XiMat	blood
44	chr10:90766800-90776600	Strong transcription	HMEC	breast
45	chr10:90767000-90772000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr10:90767000-90772400	Strong transcription	NHLF	lung
47	chr10:90767000-90772600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr10:90767000-90773000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr10:90767200-90774600	Strong transcription	Hela-S3	cervix
50	chr10:90767200-90776800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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