Variant report

Variant	rs740355
Chromosome Location	chr12:1723228-1723229
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	USF1	chr12:1722936-1723341	SK-N-SH_RA	brain:	n/a	chr12:1723199-1723210
2	SIX5	chr12:1723129-1723366	GM12878	blood:	n/a	n/a
3	ATF3	chr12:1723017-1723410	GM12878	blood:	n/a	n/a
4	USF1	chr12:1722898-1723423	HCT-116	colon:	n/a	chr12:1723199-1723210
5	HCFC1	chr12:1723003-1723727	K562	blood:	n/a	n/a
6	USF1	chr12:1722921-1723452	ECC-1	luminal epithelium:	n/a	chr12:1723199-1723210
7	USF1	chr12:1723008-1723445	H1-hESC	embryonic stem cell:	n/a	chr12:1723199-1723210
8	USF1	chr12:1723055-1723354	A549	lung:	n/a	chr12:1723199-1723210
9	JUND	chr12:1723089-1723318	K562	blood:	n/a	n/a
10	USF2	chr12:1723028-1723394	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZNF143	chr12:1723036-1723399	GM12878	blood:	n/a	n/a
12	SP4	chr12:1723074-1723319	H1-hESC	embryonic stem cell:	n/a	n/a
13	USF1	chr12:1723019-1723381	SK-N-SH	brain:	n/a	chr12:1723199-1723210
14	USF2	chr12:1723035-1723366	GM12878	blood:	n/a	n/a
15	SIX5	chr12:1723045-1723331	K562	blood:	n/a	n/a
16	USF1	chr12:1723022-1723336	SK-N-SH_RA	brain:	n/a	chr12:1723199-1723210
17	USF1	chr12:1722897-1723424	ECC-1	luminal epithelium:	n/a	chr12:1723199-1723210
18	USF2	chr12:1723078-1723353	Hela-S3	cervix:	n/a	n/a
19	SIX5	chr12:1723054-1723339	K562	blood:	n/a	n/a
20	ATF3	chr12:1723103-1723240	GM12878	blood:	n/a	n/a
21	USF1	chr12:1722996-1723384	SK-N-SH	brain:	n/a	chr12:1723199-1723210
22	ZNF143	chr12:1723020-1723419	H1-hESC	embryonic stem cell:	n/a	n/a
23	RCOR1	chr12:1723086-1723349	K562	blood:	n/a	n/a
24	ATF3	chr12:1723077-1723312	K562	blood:	n/a	n/a
25	USF1	chr12:1722976-1723269	A549	lung:	n/a	chr12:1723199-1723210
26	USF1	chr12:1723031-1723410	A549	lung:	n/a	chr12:1723199-1723210
27	SIX5	chr12:1722963-1723342	H1-hESC	embryonic stem cell:	n/a	n/a
28	ETS1	chr12:1722974-1723372	K562	blood:	n/a	n/a
29	USF1	chr12:1723076-1723294	HepG2	liver:	n/a	chr12:1723199-1723210
30	ZNF143	chr12:1723023-1723422	K562	blood:	n/a	n/a
31	USF1	chr12:1723057-1723321	HepG2	liver:	n/a	chr12:1723199-1723210
32	MYC	chr12:1723066-1723795	K562	blood:	n/a	n/a
33	USF1	chr12:1723095-1723326	GM12878	blood:	n/a	chr12:1723199-1723210
34	USF1	chr12:1723124-1723311	GM12878	blood:	n/a	chr12:1723199-1723210
35	USF1	chr12:1722951-1723377	A549	lung:	n/a	chr12:1723199-1723210
36	USF1	chr12:1722999-1723481	K562	blood:	n/a	chr12:1723199-1723210
37	USF1	chr12:1722965-1723363	K562	blood:	n/a	chr12:1723199-1723210
38	SIX5	chr12:1723110-1723351	H1-hESC	embryonic stem cell:	n/a	n/a
39	USF1	chr12:1722967-1723340	H1-hESC	embryonic stem cell:	n/a	chr12:1723199-1723210
40	USF1	chr12:1723059-1723379	A549	lung:	n/a	chr12:1723199-1723210
41	ZNF143	chr12:1723067-1723370	Hela-S3	cervix:	n/a	n/a
42	USF1	chr12:1722946-1723479	HCT-116	colon:	n/a	chr12:1723199-1723210
43	USF2	chr12:1723069-1723332	K562	blood:	n/a	n/a
44	SIX5	chr12:1723004-1723333	K562	blood:	n/a	n/a

Variant related genes	Relation type
WNT5B	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2003510	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4765829	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4765830	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765831	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7314822	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7316135	0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv3397478	chr12:1535455-1730159	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv826180	chr12:1614395-1759431	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv826181	chr12:1619798-1754941	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv898586	chr12:1690140-1734365	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv1834423	chr12:1703324-1727170	Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs740355	FGF23	cis	cerebellum	SCAN
rs740355	SLC6A12	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1715200-1723600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:1715200-1725800	Weak transcription	Esophagus	oesophagus
3	chr12:1715400-1738600	Weak transcription	Right Atrium	heart
4	chr12:1716200-1734600	Weak transcription	Fetal Stomach	stomach
5	chr12:1717000-1728800	Weak transcription	Lung	lung
6	chr12:1717800-1723600	Weak transcription	Primary B cells from cord blood	blood
7	chr12:1718200-1725200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:1719600-1725600	Weak transcription	Thymus	Thymus
9	chr12:1719600-1728000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:1720000-1725600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:1720200-1727200	Weak transcription	Fetal Intestine Small	intestine
12	chr12:1720200-1727200	Weak transcription	Stomach Mucosa	stomach
13	chr12:1720800-1725600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:1721000-1734400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:1721600-1723600	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:1721600-1723600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:1721600-1725200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:1721600-1727400	Weak transcription	Adipose Nuclei	Adipose
19	chr12:1721800-1724000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:1721800-1727200	Weak transcription	NHLF	lung
21	chr12:1721800-1727800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:1721800-1734600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:1721800-1738600	Weak transcription	Fetal Brain Female	brain
24	chr12:1722000-1724000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:1722200-1723600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:1722200-1723800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:1722200-1725800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:1722200-1727400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:1722200-1727400	Weak transcription	Osteobl	bone
30	chr12:1722200-1727600	Weak transcription	NH-A	brain
31	chr12:1722400-1723400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:1722400-1723800	Weak transcription	HSMMtube	muscle
33	chr12:1722400-1725800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:1722800-1723600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:1723000-1724800	Strong transcription	NHDF-Ad	bronchial
36	chr12:1723000-1725800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr12:1723000-1727600	Enhancers	K562	blood
38	chr12:1723200-1723800	Enhancers	HSMM	muscle

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