Variant report

Variant	rs12264390
Chromosome Location	chr10:959111-959112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:956864..959449-chr10:987864..990001,2	K562	blood:
2	chr10:951945..954088-chr10:957080..959590,3	MCF-7	breast:
3	chr10:957934..960476-chr10:961613..963216,2	K562	blood:
4	chr10:959058..959737-chr10:1016214..1016784,2	MCF-7	breast:
5	chr10:958805..960895-chr10:964152..966782,2	MCF-7	breast:
6	chr10:953280..955249-chr10:957208..959936,2	MCF-7	breast:
7	chr10:957384..959889-chr10:967554..970347,2	MCF-7	breast:
8	chr10:956519..959193-chr10:962678..964562,2	MCF-7	breast:
9	chr10:957666..959470-chr10:975640..977548,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000107929	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1013505	0.90[CEU][hapmap];1.00[ASN][1000 genomes]
rs10508208	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs10904577	1.00[ASN][1000 genomes]
rs10904580	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904581	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904583	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904584	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106064	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253444	0.89[CEU][hapmap]
rs11253445	0.90[CEU][hapmap]
rs11253446	0.90[CEU][hapmap]
rs11253458	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253459	0.88[CEU][hapmap]
rs11253460	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253465	1.00[ASN][1000 genomes]
rs11253467	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253468	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253473	1.00[ASN][1000 genomes]
rs11253475	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253485	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253488	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253492	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253493	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253494	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253495	0.94[CEU][hapmap]
rs11253499	1.00[ASN][1000 genomes]
rs11253504	0.88[CEU][hapmap]
rs11253509	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253511	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253513	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253517	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253520	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253521	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812170	1.00[ASN][1000 genomes]
rs11812523	1.00[ASN][1000 genomes]
rs11813210	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11815185	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11816064	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11817793	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11818288	1.00[ASN][1000 genomes]
rs11818325	1.00[ASN][1000 genomes]
rs12240651	1.00[ASN][1000 genomes]
rs12244253	1.00[ASN][1000 genomes]
rs12244355	1.00[ASN][1000 genomes]
rs12249634	1.00[ASN][1000 genomes]
rs12249828	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12250936	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs12250937	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs12251396	1.00[ASN][1000 genomes]
rs12254002	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12258388	1.00[ASN][1000 genomes]
rs12259338	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259720	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259801	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12260800	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12261911	1.00[ASN][1000 genomes]
rs12264711	1.00[ASN][1000 genomes]
rs12267709	1.00[ASN][1000 genomes]
rs12354639	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357633	0.90[CEU][hapmap]
rs12359645	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360270	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761424	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12762973	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12763396	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12764024	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs12765174	1.00[ASN][1000 genomes]
rs12766381	1.00[ASN][1000 genomes]
rs12768348	0.90[CEU][hapmap]
rs12769002	0.89[CEU][hapmap]
rs12769431	1.00[ASN][1000 genomes]
rs12769873	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs12770190	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs12774985	0.90[CEU][hapmap]
rs12778891	1.00[ASN][1000 genomes]
rs12783472	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377166	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs1341741	0.94[CEU][hapmap]
rs1341742	1.00[ASN][1000 genomes]
rs1539174	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555899	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs17159950	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs17159970	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs2050944	0.90[CEU][hapmap];1.00[ASN][1000 genomes]
rs34254874	1.00[ASN][1000 genomes]
rs34270014	1.00[ASN][1000 genomes]
rs34284130	1.00[ASN][1000 genomes]
rs34405399	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433840	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34847097	1.00[ASN][1000 genomes]
rs35174953	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35394603	1.00[ASN][1000 genomes]
rs35567307	1.00[ASN][1000 genomes]
rs35637113	1.00[ASN][1000 genomes]
rs35693858	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825568	1.00[ASN][1000 genomes]
rs35968821	1.00[ASN][1000 genomes]
rs4522091	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs56318703	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56347655	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61830929	1.00[ASN][1000 genomes]
rs61830932	1.00[ASN][1000 genomes]
rs7067865	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs7074642	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs7077278	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs72778229	1.00[ASN][1000 genomes]
rs765867	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs7908138	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914758	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS 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	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS 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	43 gene(s)	inside rSNPs	diseases
4	nsv949063	chr10:708293-974870	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv1043812	chr10:776547-981126	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv540406	chr10:776547-981126	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer 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	41 gene(s)	inside rSNPs	diseases
10	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
14	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
15	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
16	nsv825207	chr10:957020-1005451	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:870600-959400	Weak transcription	Stomach Mucosa	stomach
2	chr10:927600-972600	Weak transcription	Hela-S3	cervix
3	chr10:928000-963200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:928000-966400	Weak transcription	Small Intestine	intestine
5	chr10:929400-975800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:929400-976400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr10:931600-965400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr10:931600-967400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:935400-964000	Weak transcription	Psoas Muscle	Psoas
10	chr10:940000-970200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr10:940200-967600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:946000-965400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr10:946000-966600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr10:946200-965400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:947800-975400	Weak transcription	Fetal Brain Male	brain
16	chr10:949000-959800	Strong transcription	Dnd41	blood
17	chr10:949600-965400	Weak transcription	Right Ventricle	heart
18	chr10:949600-974600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr10:951000-975400	Weak transcription	Fetal Kidney	kidney
20	chr10:952600-967800	Weak transcription	Brain Angular Gyrus	brain
21	chr10:952600-971000	Weak transcription	Brain Substantia Nigra	brain
22	chr10:952600-975400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:952800-966000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:953000-965200	Weak transcription	Pancreas	Pancrea
25	chr10:953000-967400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:953000-974400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr10:954600-975000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:954800-967600	Weak transcription	NHDF-Ad	bronchial
29	chr10:954800-973600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr10:955000-965400	Weak transcription	Gastric	stomach
31	chr10:955000-967600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr10:955000-968200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr10:955000-974600	Weak transcription	Colonic Mucosa	Colon
34	chr10:955800-959600	Strong transcription	A549	lung
35	chr10:956000-967400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr10:956200-966000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:956200-972400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr10:956600-967400	Weak transcription	Colon Smooth Muscle	Colon
39	chr10:956800-970000	Weak transcription	Brain Germinal Matrix	brain
40	chr10:956800-975400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:956800-975600	Weak transcription	Fetal Brain Female	brain
42	chr10:956800-976400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr10:957000-965200	Weak transcription	Left Ventricle	heart
44	chr10:957000-967400	Weak transcription	Brain Hippocampus Middle	brain
45	chr10:957000-967400	Weak transcription	Ovary	ovary
46	chr10:957000-967800	Weak transcription	Esophagus	oesophagus
47	chr10:957000-970600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr10:957200-966000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:957200-967400	Weak transcription	HSMMtube	muscle
50	chr10:957600-966800	Weak transcription	NH-A	brain

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