Variant report

Variant	rs12222250
Chromosome Location	chr11:3954391-3954392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3952774..3955430-chr11:3970846..3973149,2	K562	blood:
2	chr11:3952025..3954655-chr11:3956750..3959173,2	MCF-7	breast:
3	chr11:3953433..3955295-chr11:3966912..3968910,2	K562	blood:

Variant related genes	Relation type
ENSG00000167323	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10430939	1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs10458900	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs10500591	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10500592	0.88[CHB][hapmap]
rs11030251	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11030286	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11030327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11030366	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11030417	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11030418	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11030453	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11030478	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs11030479	0.96[ASN][1000 genomes]
rs11030481	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs11030484	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs11030485	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs11030486	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs11030697	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs11030796	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs11525342	0.86[ASN][1000 genomes]
rs11529865	0.86[ASN][1000 genomes]
rs12224469	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1372803	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs16929410	0.81[CHB][hapmap]
rs16929438	0.82[CEU][hapmap];0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs16929467	0.88[CHB][hapmap]
rs16929477	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs16929480	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs16929488	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs16929492	0.82[CEU][hapmap];0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs16929529	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs16929531	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs16929538	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs16929540	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs16929542	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs16929546	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs16929611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16929616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16929653	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1822286	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs1899478	0.81[ASN][1000 genomes]
rs2167563	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3750994	0.82[CEU][hapmap];0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs4910878	0.88[CHB][hapmap]
rs55679086	0.96[ASN][1000 genomes]
rs55978228	0.96[ASN][1000 genomes]
rs56126231	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56140937	0.80[ASN][1000 genomes]
rs59195871	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59242983	0.82[ASN][1000 genomes]
rs60930198	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61897162	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61897163	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897164	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897166	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61897167	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61897170	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61897171	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61897194	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61897195	0.95[ASN][1000 genomes]
rs61897201	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61897202	0.96[ASN][1000 genomes]
rs61897203	0.83[ASN][1000 genomes]
rs61897234	0.85[ASN][1000 genomes]
rs61897237	0.84[ASN][1000 genomes]
rs61897238	0.82[ASN][1000 genomes]
rs61897254	0.80[ASN][1000 genomes]
rs6578423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs723779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs72847181	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72851736	0.96[ASN][1000 genomes]
rs750526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928117	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7934581	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs7941743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs894454	0.82[CEU][hapmap];0.88[CHB][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv1043039	chr11:3903226-3955159	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv896895	chr11:3942001-3972236	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3938400-3956400	Weak transcription	Dnd41	blood
2	chr11:3939000-3956000	Weak transcription	Esophagus	oesophagus
3	chr11:3943400-3954800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:3948200-3955800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:3948200-3955800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:3948400-3960400	Weak transcription	NHEK	skin
7	chr11:3948600-3955600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:3948800-3954400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:3948800-3960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:3949000-3961400	Weak transcription	Right Atrium	heart
11	chr11:3949400-3959400	Weak transcription	Fetal Lung	lung
12	chr11:3950000-3957600	Weak transcription	GM12878-XiMat	blood
13	chr11:3950400-3972200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr11:3950800-3956200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:3951000-3954600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr11:3951000-3955600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:3951000-3957400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:3951000-3960600	Weak transcription	Stomach Mucosa	stomach
19	chr11:3951200-3954800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:3951200-3965400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:3951200-3967600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:3951400-3955000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:3951400-3955600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:3951400-3955800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:3951400-3955800	Weak transcription	Fetal Stomach	stomach
26	chr11:3951400-3956000	Weak transcription	Aorta	Aorta
27	chr11:3951400-3956000	Weak transcription	Gastric	stomach
28	chr11:3951400-3956400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:3951400-3959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:3951400-3959200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:3951400-3959800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:3951400-3961400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr11:3951400-3963400	Weak transcription	A549	lung
34	chr11:3951400-3963600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr11:3951600-3954800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:3951600-3955400	Weak transcription	Right Ventricle	heart
37	chr11:3951600-3959800	Weak transcription	Adipose Nuclei	Adipose
38	chr11:3951600-3963400	Weak transcription	Brain Hippocampus Middle	brain
39	chr11:3951800-3956000	Weak transcription	Left Ventricle	heart
40	chr11:3951800-3959600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:3952000-3955400	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:3952000-3955600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr11:3952000-3963400	Weak transcription	Pancreas	Pancrea
44	chr11:3952200-3954400	Weak transcription	Liver	Liver
45	chr11:3952200-3955000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr11:3952200-3961000	Weak transcription	Fetal Muscle Leg	muscle
47	chr11:3952400-3955000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:3952600-3954400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:3952600-3954600	Weak transcription	Fetal Heart	heart
50	chr11:3952800-3954400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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