Variant report

Variant	rs12022014
Chromosome Location	chr1:239882446-239882447
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	MYC	chr1:239881907-239883553	NB4	blood:	n/a	chr1:239883185-239883195
2	POLR2A	chr1:239882270-239883651	NB4	blood:	n/a	n/a
3	MAX	chr1:239881010-239883868	NB4	blood:	n/a	chr1:239883185-239883195

Variant related genes	Relation type
CHRM3-AS2	TF binding region
CHRM3	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10429915	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10429917	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10429918	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802792	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10925945	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10925962	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12021900	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12028626	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030687	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12033242	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047255	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117703	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118615	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12130233	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143018	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832154	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3936418	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72632884	0.82[EUR][1000 genomes]
rs72632885	0.94[ASN][1000 genomes]
rs72632886	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2757778	chr1:239766094-240389504	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv2759009	chr1:239766094-240389504	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239870200-239883000	Weak transcription	Fetal Brain Male	brain
2	chr1:239870200-239883000	Weak transcription	Gastric	stomach
3	chr1:239875400-239890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:239878200-239891000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:239879400-239882800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:239880000-239885800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:239880400-239884000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:239880400-239885600	Active TSS	Primary T cells fromperipheralblood	blood
9	chr1:239880600-239884600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:239880800-239882800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:239880800-239883800	Active TSS	Duodenum Mucosa	Duodenum
12	chr1:239881000-239884200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:239881000-239884400	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr1:239881000-239885400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr1:239881200-239882600	Weak transcription	Stomach Mucosa	stomach
16	chr1:239881200-239883000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:239881200-239883000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:239881200-239884200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:239881200-239884400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr1:239881400-239882800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:239881400-239884800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:239881600-239882600	Active TSS	Dnd41	blood
23	chr1:239881800-239883000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:239881800-239883200	Flanking Active TSS	Fetal Thymus	thymus
25	chr1:239881800-239883400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr1:239881800-239884600	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr1:239882000-239882600	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:239882200-239882800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:239882200-239883000	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr1:239882200-239883000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr1:239882200-239883200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:239882200-239883600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr1:239882200-239884000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr1:239882200-239884200	Active TSS	Primary B cells from cord blood	blood
35	chr1:239882400-239882600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:239882400-239882800	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr1:239882400-239882800	Weak transcription	Brain Angular Gyrus	brain
38	chr1:239882400-239883000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr1:239882400-239883000	Flanking Active TSS	Thymus	Thymus
40	chr1:239882400-239883200	Enhancers	Primary B cells from peripheral blood	blood
41	chr1:239882400-239883200	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr1:239882400-239883400	Enhancers	Pancreas	Pancrea
43	chr1:239882400-239883600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr1:239882400-239885000	Active TSS	Primary T helper naive cells from peripheral blood	blood

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