Variant report

Variant	rs12259713
Chromosome Location	chr10:91094315-91094316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:91086403..91089519-chr10:91091273..91094339,4	K562	blood:
2	chr10:91093291..91095702-chr10:91097071..91099553,2	MCF-7	breast:
3	chr10:91094086..91096049-chr10:91100539..91102838,2	MCF-7	breast:
4	chr10:91092012..91093700-chr10:91094311..91097149,2	K562	blood:

Variant related genes	Relation type
ENSG00000119917	Chromatin interaction
ENSG00000107798	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10159512	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159516	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10159652	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159694	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159869	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159879	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1041540	1.00[ASN][1000 genomes]
rs11203074	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203076	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11203077	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203081	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203084	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203085	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203087	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11203088	1.00[ASN][1000 genomes]
rs11203097	1.00[ASN][1000 genomes]
rs12241343	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242568	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244506	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12244571	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245627	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249661	1.00[ASN][1000 genomes]
rs12249707	1.00[ASN][1000 genomes]
rs12250753	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12250860	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12251895	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256980	0.89[AFR][1000 genomes]
rs12259768	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261273	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263989	1.00[ASN][1000 genomes]
rs12264051	1.00[ASN][1000 genomes]
rs12266581	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12267943	1.00[ASN][1000 genomes]
rs1332332	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332333	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332334	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1332336	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332337	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119593	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119665	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119672	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119790	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119791	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2151008	1.00[ASN][1000 genomes]
rs41284140	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41284142	1.00[ASN][1000 genomes]
rs4378299	1.00[ASN][1000 genomes]
rs6586185	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6586186	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586187	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6586189	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586190	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586191	1.00[ASN][1000 genomes]
rs7081163	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7088379	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099668	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099681	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100115	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367441	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73367444	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367447	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367460	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73368528	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7898580	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7901862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7902096	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7902109	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7902380	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7904924	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7906827	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7907230	0.89[AFR][1000 genomes]
rs7907341	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7911396	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916398	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7917725	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663337	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663529	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663533	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv1040375	chr10:91022218-91153074	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv34085	chr10:91065949-91174175	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91088000-91099800	Weak transcription	Gastric	stomach
2	chr10:91090200-91107600	Weak transcription	Pancreas	Pancrea
3	chr10:91092600-91095000	Enhancers	Dnd41	blood
4	chr10:91092600-91095600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr10:91092800-91095000	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:91092800-91095000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr10:91092800-91095200	Enhancers	Spleen	Spleen
8	chr10:91092800-91095400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr10:91092800-91095400	Enhancers	Small Intestine	intestine
10	chr10:91092800-91095600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr10:91093000-91094800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr10:91093000-91095200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr10:91093000-91095200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr10:91093200-91094600	Enhancers	Ovary	ovary
15	chr10:91093200-91095600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:91093400-91095600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr10:91093400-91097200	Enhancers	Brain Substantia Nigra	brain
18	chr10:91093400-91097800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr10:91093400-91100200	Weak transcription	K562	blood
20	chr10:91093400-91100800	Weak transcription	Right Ventricle	heart
21	chr10:91093600-91096600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr10:91093800-91094400	Enhancers	Brain Hippocampus Middle	brain
23	chr10:91093800-91094800	Active TSS	GM12878-XiMat	blood
24	chr10:91093800-91095400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr10:91093800-91097200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:91093800-91097400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr10:91093800-91099000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr10:91093800-91106000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:91093800-91106400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr10:91094000-91094400	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr10:91094000-91094400	Weak transcription	Lung	lung
32	chr10:91094000-91094800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr10:91094000-91095000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr10:91094000-91095000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:91094000-91095000	Weak transcription	Colon Smooth Muscle	Colon
36	chr10:91094000-91095200	Weak transcription	Fetal Heart	heart
37	chr10:91094000-91095400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr10:91094000-91095400	Enhancers	Fetal Intestine Small	intestine
39	chr10:91094000-91095600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr10:91094000-91095800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr10:91094000-91095800	Enhancers	Fetal Intestine Large	intestine
42	chr10:91094000-91096200	Weak transcription	Hela-S3	cervix
43	chr10:91094000-91097200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr10:91094000-91097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:91094000-91097200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:91094000-91097200	Enhancers	Brain Anterior Caudate	brain
47	chr10:91094000-91097200	Weak transcription	NH-A	brain
48	chr10:91094000-91097400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr10:91094000-91097400	Weak transcription	NHLF	lung
50	chr10:91094000-91098000	Weak transcription	HSMMtube	muscle

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