Variant report

Variant	rs12403033
Chromosome Location	chr1:86862991-86862992
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	MXI1	chr1:86860760-86863066	SK-N-SH	brain:	n/a	chr1:86861997-86862012

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86821077..86823352-chr1:86861196..86863227,2	K562	blood:

Variant related genes	Relation type
ODF2L	TF binding region
ENSG00000122417	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10493790	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11161810	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161814	0.91[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161816	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161817	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161831	0.87[CEU][hapmap]
rs1158833	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1182098	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1182099	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1182101	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12119411	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12123660	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125965	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12130284	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12145243	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12146009	0.85[CEU][hapmap]
rs12406320	0.91[CEU][hapmap];0.92[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1323036	0.85[AMR][1000 genomes]
rs1413431	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1413432	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17409213	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17409304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17449526	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1814203	0.83[CEU][hapmap]
rs1931360	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1931361	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1931362	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs272486	0.84[AMR][1000 genomes]
rs272488	0.90[ASN][1000 genomes]
rs272489	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs272490	0.93[ASN][1000 genomes]
rs272493	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272495	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272496	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272497	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272499	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272500	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs272501	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272505	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272506	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs272509	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272512	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272514	0.96[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs272515	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272518	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35489949	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3737673	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3765983	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs421105	0.91[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs423991	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5026277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56104000	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56408800	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57210989	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61124915	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6688340	0.85[AMR][1000 genomes]
rs72720116	0.83[AMR][1000 genomes]
rs72720129	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs977919	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86860800-86863000	Active TSS	Colonic Mucosa	Colon
2	chr1:86861400-86863000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:86862200-86863000	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr1:86862200-86863000	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr1:86862200-86863000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr1:86862200-86863000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:86862200-86863000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr1:86862200-86863200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:86862400-86863000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:86862400-86863000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr1:86862400-86863000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr1:86862400-86863000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:86862400-86863000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:86862400-86863000	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr1:86862400-86863000	Flanking Active TSS	Fetal Brain Female	brain
16	chr1:86862400-86863000	Flanking Active TSS	Dnd41	blood
17	chr1:86862400-86863200	Enhancers	Small Intestine	intestine
18	chr1:86862400-86876400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:86862600-86863000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:86862600-86863000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr1:86862600-86863000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:86862600-86863000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:86862600-86863000	Enhancers	Fetal Intestine Large	intestine
24	chr1:86862600-86863000	Enhancers	Fetal Intestine Small	intestine
25	chr1:86862600-86863000	Enhancers	Fetal Muscle Leg	muscle
26	chr1:86862600-86863000	Enhancers	Placenta	Placenta
27	chr1:86862600-86863000	Enhancers	Pancreas	Pancrea
28	chr1:86862600-86863000	Enhancers	Rectal Smooth Muscle	rectum
29	chr1:86862600-86863000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr1:86862600-86863200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:86862600-86864200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:86862800-86863000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:86862800-86863000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:86862800-86863000	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr1:86862800-86863000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:86862800-86863000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:86862800-86863000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:86862800-86863000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr1:86862800-86863000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr1:86862800-86863000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:86862800-86863000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:86862800-86863000	Enhancers	Brain Angular Gyrus	brain
43	chr1:86862800-86863000	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr1:86862800-86863000	Active TSS	Brain Cingulate Gyrus	brain
45	chr1:86862800-86863000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr1:86862800-86863000	Enhancers	Duodenum Mucosa	Duodenum
47	chr1:86862800-86863000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr1:86862800-86863000	Enhancers	Fetal Kidney	kidney
49	chr1:86862800-86863000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr1:86862800-86863000	Enhancers	Fetal Lung	lung

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