Variant report

Variant	rs2525448
Chromosome Location	chr12:47985899-47985900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr12:47985482-47985915	HL-60	blood:	n/a	chr12:47985689-47985702 chr12:47985692-47985699 chr12:47985695-47985704
2	SPI1	chr12:47985440-47986106	GM12878	blood:	n/a	chr12:47985689-47985702 chr12:47985692-47985699 chr12:47985695-47985704
3	FOXP2	chr12:47985670-47985916	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47978595..47981359-chr12:47984602..47986611,2	K562	blood:

Variant related genes	Relation type
ENSG00000257905	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10875679	0.92[AMR][1000 genomes]
rs1153975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1232968	0.83[AMR][1000 genomes]
rs1232976	0.90[AMR][1000 genomes]
rs1232977	0.81[AMR][1000 genomes]
rs1232980	0.80[ASN][1000 genomes]
rs1232981	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1232982	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1232983	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1232985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1232986	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1232987	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1233045	0.92[AMR][1000 genomes]
rs1233046	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs1233047	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes]
rs1233049	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1233050	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1233052	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs1233053	0.85[AMR][1000 genomes]
rs1233055	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs1233061	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1235151	0.92[AMR][1000 genomes]
rs1237842	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2022526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2022527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2155794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2155795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2524317	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2525449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2847431	1.00[ASN][1000 genomes]
rs2847433	0.92[AMR][1000 genomes]
rs2847434	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587577	0.93[ASN][1000 genomes]
rs590089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs603042	0.87[ASN][1000 genomes]
rs605026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs611208	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs612096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs618038	0.86[ASN][1000 genomes]
rs61917588	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61919786	0.93[ASN][1000 genomes]
rs622728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs623947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs628070	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs652457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs652543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs652898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs653843	0.91[ASN][1000 genomes]
rs657246	0.93[ASN][1000 genomes]
rs663945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs667610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs681100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs682782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs688815	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs727121	0.99[ASN][1000 genomes]
rs948392	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes]
rs948394	0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv832400	chr12:47840248-48024605	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1051131	chr12:47883981-48016556	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv899056	chr12:47940764-48012390	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv558786	chr12:47942029-48044011	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv558788	chr12:47945797-48012390	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2761737	chr12:47946795-48045722	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1053061	chr12:47946795-48045722	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv899057	chr12:47947551-48012390	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv527728	chr12:47954597-48044506	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47978000-47986000	Enhancers	Colon Smooth Muscle	Colon
2	chr12:47981000-47986000	Enhancers	Rectal Smooth Muscle	rectum
3	chr12:47983200-47986000	Enhancers	Fetal Kidney	kidney
4	chr12:47984200-47986000	Enhancers	NHDF-Ad	bronchial
5	chr12:47984600-47986000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:47984600-47986000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:47984600-47986000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:47984600-47986200	Enhancers	Fetal Lung	lung
9	chr12:47984600-47986400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr12:47984600-47986800	Enhancers	Brain Hippocampus Middle	brain
11	chr12:47984800-47986000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr12:47984800-47986000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:47984800-47986000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:47984800-47986000	Enhancers	Brain Cingulate Gyrus	brain
15	chr12:47984800-47986000	Enhancers	Brain Germinal Matrix	brain
16	chr12:47984800-47986600	Enhancers	Fetal Muscle Trunk	muscle
17	chr12:47985000-47986000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:47985000-47986000	Enhancers	Adipose Nuclei	Adipose
19	chr12:47985000-47986000	Enhancers	Fetal Brain Male	brain
20	chr12:47985200-47986000	Enhancers	Brain Angular Gyrus	brain
21	chr12:47985200-47986000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr12:47985200-47986000	Enhancers	Fetal Brain Female	brain
23	chr12:47985200-47986000	Enhancers	Fetal Muscle Leg	muscle
24	chr12:47985200-47986000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr12:47985400-47986000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr12:47985400-47986000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:47985400-47986000	Enhancers	Duodenum Mucosa	Duodenum
28	chr12:47985400-47986000	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr12:47985400-47986000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr12:47985400-47986000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:47985400-47986000	Enhancers	NHLF	lung
32	chr12:47985600-47986000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:47985600-47986000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:47985600-47986000	Enhancers	Brain Substantia Nigra	brain
35	chr12:47985600-47986000	Enhancers	Lung	lung
36	chr12:47985600-47986000	Enhancers	Right Atrium	heart
37	chr12:47985600-47986000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr12:47985600-47986000	Enhancers	Stomach Smooth Muscle	stomach
39	chr12:47985800-47986000	Enhancers	Brain Anterior Caudate	brain
40	chr12:47985800-47986000	Active TSS	HSMMtube	muscle
41	chr12:47985800-47986200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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