Variant report

Variant	rs7086446
Chromosome Location	chr10:93878609-93878610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BTAF1-2	chr10:93878421-93878921	NONHSAT015645

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10786028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882025	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10882030	0.81[EUR][1000 genomes]
rs10882031	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs11186815	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11186817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11186818	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11186822	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11186829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186830	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186834	0.83[ASN][1000 genomes]
rs11186835	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186836	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11186838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186839	0.84[EUR][1000 genomes]
rs11186841	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs11186843	0.84[EUR][1000 genomes]
rs11186856	0.82[CEU][hapmap]
rs11527871	0.82[CHB][hapmap]
rs12357187	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12571139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1539468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1557178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1571176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878424	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1935865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2096227	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2105364	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2185834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2421831	0.84[EUR][1000 genomes]
rs2421874	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34658839	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781230	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs3781231	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3781233	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4933712	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4933717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56345827	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56705680	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61875208	0.82[EUR][1000 genomes]
rs6583802	0.84[EUR][1000 genomes]
rs66636110	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7067935	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs7069149	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7071524	0.84[EUR][1000 genomes]
rs7079499	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7084059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7085684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7096357	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs766398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs766399	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7905301	0.80[EUR][1000 genomes]
rs9794362	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051226	chr10:93711296-93915586	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540745	chr10:93711296-93915586	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv948137	chr10:93876652-93879263	Weak transcription Enhancers Genic enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93841200-93881600	Weak transcription	Esophagus	oesophagus
2	chr10:93859200-93901400	Weak transcription	Primary B cells from cord blood	blood
3	chr10:93861400-93879000	Weak transcription	Adipose Nuclei	Adipose
4	chr10:93862000-93881400	Weak transcription	Colon Smooth Muscle	Colon
5	chr10:93862000-93881400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr10:93862000-93883200	Weak transcription	Fetal Stomach	stomach
7	chr10:93863800-93879200	Weak transcription	GM12878-XiMat	blood
8	chr10:93863800-93881400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr10:93863800-93881600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr10:93867400-93881800	Weak transcription	Stomach Mucosa	stomach
11	chr10:93868000-93901800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:93870800-93881400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr10:93871000-93881600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr10:93871000-93881800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:93871000-93882400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:93871000-93882400	Weak transcription	Primary T cells from cord blood	blood
17	chr10:93871000-93887200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr10:93871400-93879000	Weak transcription	Brain Substantia Nigra	brain
19	chr10:93871400-93881400	Weak transcription	Brain Anterior Caudate	brain
20	chr10:93871600-93882000	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:93871800-93881400	Weak transcription	Aorta	Aorta
22	chr10:93871800-93881600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr10:93871800-93884400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr10:93872400-93881400	Weak transcription	Left Ventricle	heart
25	chr10:93873000-93881400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr10:93873600-93881400	Weak transcription	Ovary	ovary
27	chr10:93873600-93882000	Weak transcription	Lung	lung
28	chr10:93873600-93883000	Weak transcription	Right Atrium	heart
29	chr10:93874000-93881400	Weak transcription	Right Ventricle	heart
30	chr10:93874000-93883000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr10:93874000-93885000	Weak transcription	Small Intestine	intestine
32	chr10:93874200-93881400	Weak transcription	Fetal Heart	heart
33	chr10:93874400-93882800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr10:93874600-93883000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr10:93874600-93899600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr10:93875000-93882600	Weak transcription	Fetal Intestine Large	intestine
37	chr10:93875000-93883800	Weak transcription	Fetal Intestine Small	intestine
38	chr10:93878200-93885000	Enhancers	Liver	Liver
39	chr10:93878400-93878800	Enhancers	Pancreas	Pancrea
40	chr10:93878400-93879200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr10:93878400-93879400	Enhancers	Psoas Muscle	Psoas
42	chr10:93878400-93881600	Enhancers	HepG2	liver
43	chr10:93878600-93878800	Enhancers	Brain Angular Gyrus	brain
44	chr10:93878600-93878800	Genic enhancers	Gastric	stomach

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