Variant report

Variant	rs740024
Chromosome Location	chr12:48382282-48382283
allele	G/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	TCF12	chr12:48381933-48382621	ECC-1	luminal epithelium:	n/a	chr12:48382585-48382595
2	ESR1	chr12:48382042-48382445	ECC-1	luminal epithelium:	n/a	n/a
3	ESR1	chr12:48382082-48382457	ECC-1	luminal epithelium:	n/a	n/a
4	ESR1	chr12:48381982-48382556	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr12:48382226-48382595	H1-hESC	embryonic stem cell:	n/a	chr12:48382370-48382379 chr12:48382366-48382375
6	ESR1	chr12:48381949-48382522	ECC-1	luminal epithelium:	n/a	n/a
7	REST	chr12:48382051-48382782	H1-neurons	neurons:	n/a	n/a
8	ZBTB7A	chr12:48381787-48382613	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr12:48382194-48382522	H1-hESC	embryonic stem cell:	n/a	chr12:48382370-48382379 chr12:48382366-48382375
10	ESR1	chr12:48382077-48382530	ECC-1	luminal epithelium:	n/a	n/a
11	SIN3A	chr12:48382230-48382596	H1-hESC	embryonic stem cell:	n/a	n/a
12	EP300	chr12:48381933-48382579	ECC-1	luminal epithelium:	n/a	chr12:48382138-48382152 chr12:48382144-48382158

Variant related genes	Relation type
COL2A1	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11168337	0.85[CHD][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1621710	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1635534	0.90[ASN][1000 genomes]
rs1635535	0.90[ASN][1000 genomes]
rs1635536	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1635537	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635544	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1635546	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1635547	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1635553	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1793911	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793912	0.89[ASN][1000 genomes]
rs1793913	0.89[ASN][1000 genomes]
rs1793915	0.89[ASN][1000 genomes]
rs1793917	0.86[ASN][1000 genomes]
rs1793923	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1793924	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276454	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs2276456	0.82[CHB][hapmap]
rs3829734	0.87[ASN][1000 genomes]
rs3829736	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs917055	0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs740024	PRICKLE1	cis	parietal	SCAN
rs740024	SNORA2A	cis	parietal	SCAN
rs740024	C12orf68	cis	parietal	SCAN
rs740024	PRKAG1	cis	parietal	SCAN
rs740024	PRPF40B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
3	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
4	chr12:48381000-48383600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:48381200-48382600	Enhancers	Fetal Brain Male	brain
6	chr12:48381200-48385400	Enhancers	Fetal Muscle Leg	muscle
7	chr12:48381200-48385800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:48381400-48382400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:48381400-48382600	Bivalent Enhancer	Fetal Stomach	stomach
10	chr12:48381400-48383800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:48381400-48384400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:48381400-48386400	Enhancers	Primary B cells from peripheral blood	blood
13	chr12:48381400-48386800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:48381400-48388800	Weak transcription	Fetal Intestine Small	intestine
15	chr12:48381600-48382600	Enhancers	Fetal Brain Female	brain
16	chr12:48381600-48383000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
17	chr12:48381600-48383200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:48381600-48383200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:48381800-48382400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:48381800-48382600	Enhancers	Adipose Nuclei	Adipose
21	chr12:48381800-48382800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr12:48381800-48382800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:48381800-48383000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
24	chr12:48381800-48383000	Weak transcription	Fetal Thymus	thymus
25	chr12:48381800-48383800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:48381800-48383800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:48381800-48383800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr12:48382000-48382400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:48382000-48382400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr12:48382000-48382600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr12:48382000-48382600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
32	chr12:48382000-48382600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:48382000-48382800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:48382000-48383000	Enhancers	Brain Germinal Matrix	brain
35	chr12:48382000-48383200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:48382200-48382400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
37	chr12:48382200-48382600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:48382200-48382600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:48382200-48383000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr12:48382200-48383200	Weak transcription	Primary B cells from cord blood	blood
41	chr12:48382200-48385000	Weak transcription	Right Atrium	heart

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