Variant report

Variant	rs12258585
Chromosome Location	chr10:43640914-43640915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43634643..43637619-chr10:43638128..43641213,3	K562	blood:
2	chr10:43633265..43635390-chr10:43638781..43641016,3	MCF-7	breast:
3	chr10:43632375..43637619-chr10:43637956..43641272,5	K562	blood:

Variant related genes	Relation type
ENSG00000273008	Chromatin interaction
ENSG00000169826	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10159558	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11238441	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11238465	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12260994	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12262152	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12765436	0.82[ASN][1000 genomes]
rs12765715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12765838	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12766298	0.82[ASN][1000 genomes]
rs12775330	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12775743	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12779732	0.82[ASN][1000 genomes]
rs17363630	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1799939	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1800863	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864393	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1879299	0.82[AMR][1000 genomes]
rs2075911	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28401552	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2900627	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3026776	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3026779	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3026781	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3026782	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34817887	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987091	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7074319	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7086299	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7092548	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7096367	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71505665	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71505667	0.82[ASN][1000 genomes]
rs71505668	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72783237	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72783242	0.82[ASN][1000 genomes]
rs7893332	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7903283	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7910648	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7910805	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7921281	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7923256	0.88[AMR][1000 genomes]
rs9804209	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv1038102	chr10:43441601-43642908	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1051701	chr10:43555542-43642895	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1042310	chr10:43623060-43688505	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43634800-43641000	Weak transcription	Stomach Mucosa	stomach
2	chr10:43634800-43646800	Weak transcription	Left Ventricle	heart
3	chr10:43634800-43652200	Weak transcription	Gastric	stomach
4	chr10:43635000-43641600	Weak transcription	Psoas Muscle	Psoas
5	chr10:43635200-43641800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr10:43635400-43641200	Weak transcription	Brain Substantia Nigra	brain
7	chr10:43635400-43642400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:43635400-43644200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:43635400-43655600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:43635600-43647000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:43635600-43689000	Weak transcription	Esophagus	oesophagus
12	chr10:43635800-43642000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr10:43636000-43641800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr10:43636200-43641600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr10:43636400-43647000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr10:43636600-43641000	Weak transcription	A549	lung
17	chr10:43636600-43641400	Weak transcription	Brain Germinal Matrix	brain
18	chr10:43636600-43641800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:43636600-43642200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr10:43636600-43646800	Weak transcription	NHLF	lung
21	chr10:43636600-43654800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr10:43636600-43655600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr10:43637200-43641400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr10:43637400-43641600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:43637400-43642000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr10:43637400-43647000	Weak transcription	HSMMtube	muscle
27	chr10:43637400-43655200	Weak transcription	HSMM	muscle
28	chr10:43637600-43651200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr10:43637600-43652200	Weak transcription	Fetal Thymus	thymus
30	chr10:43637800-43641200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr10:43638000-43642000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr10:43638200-43643800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:43638200-43646800	Weak transcription	Thymus	Thymus
34	chr10:43638600-43641200	Weak transcription	Primary B cells from cord blood	blood
35	chr10:43638600-43645800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr10:43638600-43649000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr10:43639000-43641200	Enhancers	Primary T cells from cord blood	blood
38	chr10:43639000-43642000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr10:43639000-43644400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr10:43639400-43641000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr10:43639400-43647000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr10:43639400-43650600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr10:43639600-43641600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr10:43639600-43647000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr10:43640000-43641600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr10:43640000-43641800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr10:43640400-43641000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr10:43640400-43641000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr10:43640400-43641000	Enhancers	Osteobl	bone
50	chr10:43640400-43641400	Enhancers	GM12878-XiMat	blood

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