Variant report

Variant	rs5008753
Chromosome Location	chr1:67092248-67092249
allele	A/G
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	GATA3	chr1:67091627-67092624	SK-N-SH	brain:	n/a	n/a
2	EP300	chr1:67091758-67092546	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:67091671-67092575	SK-N-SH	brain:	n/a	n/a
4	EP300	chr1:67091843-67092410	SK-N-SH_RA	brain:	n/a	n/a
5	NFIC	chr1:67091748-67092553	SK-N-SH	brain:	n/a	n/a
6	EP300	chr1:67091609-67092628	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr1:67091877-67092472	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr1:67091805-67092548	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr1:67091851-67092383	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr1:67091879-67092443	SK-N-SH	brain:	n/a	n/a
11	PBX3	chr1:67091860-67092474	SK-N-SH	brain:	n/a	n/a
12	PBX3	chr1:67091849-67092491	SK-N-SH	brain:	n/a	n/a
13	EP300	chr1:67091840-67092396	SK-N-SH_RA	brain:	n/a	n/a
14	GATA3	chr1:67091735-67092531	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67088339..67090517-chr1:67091923..67094068,2	K562	blood:

Variant related genes	Relation type
MIR3117	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10128053	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs10749764	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs11208913	0.81[ASN][1000 genomes]
rs11208922	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11208940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs12057164	0.83[ASN][1000 genomes]
rs12062570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12066541	0.82[ASN][1000 genomes]
rs12069946	0.90[JPT][hapmap]
rs12070270	0.90[JPT][hapmap]
rs12072937	0.90[JPT][hapmap]
rs12074963	0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12085282	0.89[JPT][hapmap]
rs12091471	0.90[JPT][hapmap]
rs12091475	0.90[JPT][hapmap]
rs12094526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs13376692	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs1530490	0.83[ASN][1000 genomes]
rs1530491	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs17129101	0.90[JPT][hapmap]
rs17129226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17129244	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17129245	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17129252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17129269	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17129307	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs20354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2121042	0.81[ASN][1000 genomes]
rs2166307	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs2166308	0.81[ASN][1000 genomes]
rs2182110	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3901541	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs41405244	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs41418445	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs41511845	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4655639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655642	0.89[CHB][hapmap];0.90[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57572851	1.00[ASN][1000 genomes]
rs58064608	0.91[ASN][1000 genomes]
rs6588210	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6588211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6588212	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6588213	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs66552897	0.81[ASN][1000 genomes]
rs6664698	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6670827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6689183	0.87[ASN][1000 genomes]
rs6694782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs67915022	0.81[ASN][1000 genomes]
rs72669451	1.00[ASN][1000 genomes]
rs72676189	0.83[ASN][1000 genomes]
rs72676194	0.90[ASN][1000 genomes]
rs72676196	0.90[ASN][1000 genomes]
rs72676198	0.81[ASN][1000 genomes]
rs72679015	0.94[ASN][1000 genomes]
rs7520353	0.90[JPT][hapmap]
rs7528240	0.83[ASN][1000 genomes]
rs7531750	0.80[ASN][1000 genomes]
rs7536634	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7538967	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7540244	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs7543378	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7545674	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs920986	1.00[JPT][hapmap]
rs9787219	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1221	chr1:67047908-67092696	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5008753	IL23R	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67071600-67094800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:67084200-67099800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:67088400-67114200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:67089800-67092600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
6	chr1:67090800-67094600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:67090800-67099600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:67090800-67108400	Weak transcription	Brain Anterior Caudate	brain
9	chr1:67091000-67099000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:67091200-67100800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:67091200-67100800	Weak transcription	NHLF	lung
12	chr1:67091200-67107400	Weak transcription	NHDF-Ad	bronchial
13	chr1:67091200-67108600	Weak transcription	Osteobl	bone
14	chr1:67091200-67108800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:67091200-67128000	Weak transcription	NH-A	brain
16	chr1:67091400-67093200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:67091400-67098200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:67091400-67105200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:67091400-67107400	Weak transcription	Fetal Brain Female	brain
20	chr1:67091600-67094000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:67092000-67092400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:67092000-67092600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:67092000-67093200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:67092000-67117200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:67092200-67092600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:67092200-67092600	Strong transcription	Aorta	Aorta
27	chr1:67092200-67092800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:67092200-67099800	Weak transcription	Psoas Muscle	Psoas
29	chr1:67092200-67114200	Weak transcription	Primary hematopoietic stem cells	blood

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