Variant report

Variant	rs17128012
Chromosome Location	chr1:86101340-86101341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10791	0.88[JPT][hapmap];0.82[TSI][hapmap]
rs12563027	0.81[JPT][hapmap]
rs12563476	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12563666	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12564057	0.84[ASN][1000 genomes]
rs12564166	0.95[EUR][1000 genomes]
rs12564468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12565129	0.89[ASN][1000 genomes]
rs12566306	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs1360240	0.97[ASN][1000 genomes]
rs17128092	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17128152	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17128155	1.00[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17128257	0.81[JPT][hapmap]
rs2297138	1.00[ASW][hapmap]
rs2297139	1.00[ASW][hapmap]
rs3767161	0.81[CHB][hapmap]
rs41331746	0.81[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs72946648	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72946655	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1000290	chr1:86078495-86105379	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17128012	ODF2L	cis	temporal cortex	BrainEAC

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86083800-86103200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:86088200-86101800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:86088400-86101400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:86088400-86102000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:86088400-86103000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:86088600-86101800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:86088600-86103000	Weak transcription	NHEK	skin
8	chr1:86088800-86101800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:86088800-86101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:86089400-86102600	Weak transcription	GM12878-XiMat	blood
11	chr1:86089400-86103000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:86091200-86103200	Weak transcription	Brain Angular Gyrus	brain
13	chr1:86091800-86102400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:86091800-86107600	Weak transcription	Colonic Mucosa	Colon
15	chr1:86092200-86102000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:86093200-86102400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:86094000-86118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:86094800-86102000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:86094800-86103200	Weak transcription	Small Intestine	intestine
20	chr1:86095000-86102000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:86095000-86102400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:86095000-86102800	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:86095000-86103200	Weak transcription	Fetal Heart	heart
24	chr1:86095200-86101800	Weak transcription	Fetal Intestine Small	intestine
25	chr1:86095200-86101800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:86095200-86102000	Weak transcription	Esophagus	oesophagus
27	chr1:86095200-86102000	Weak transcription	Fetal Intestine Large	intestine
28	chr1:86095200-86102400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:86095200-86102600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:86095200-86102800	Weak transcription	Fetal Stomach	stomach
31	chr1:86095200-86103000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:86095200-86103000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:86095200-86103000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:86095200-86103000	Weak transcription	Gastric	stomach
35	chr1:86095200-86103000	Weak transcription	Ovary	ovary
36	chr1:86095200-86103000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:86095200-86103000	Weak transcription	Spleen	Spleen
38	chr1:86095200-86104200	Weak transcription	Psoas Muscle	Psoas
39	chr1:86095200-86104400	Weak transcription	Right Ventricle	heart
40	chr1:86095400-86101800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:86095400-86101800	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:86095400-86102600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:86095400-86102800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:86095400-86103000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:86095400-86103000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:86095400-86103000	Weak transcription	Brain Anterior Caudate	brain
47	chr1:86095400-86103000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:86095400-86107600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:86095400-86119000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion

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