Variant report

Variant	rs1000824
Chromosome Location	chr12:9064374-9064375
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	JUND	chr12:9064168-9064969	H1-hESC	embryonic stem cell:	n/a	chr12:9064292-9064301
2	SP1	chr12:9064125-9064913	H1-hESC	embryonic stem cell:	n/a	n/a
3	SRF	chr12:9064327-9064715	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD2	chr12:9064075-9064969	H1-hESC	embryonic stem cell:	n/a	n/a
5	EP300	chr12:9064148-9064957	H1-hESC	embryonic stem cell:	n/a	chr12:9064294-9064303
6	TAF7	chr12:9064014-9067029	H1-hESC	embryonic stem cell:	n/a	n/a
7	HDAC2	chr12:9064133-9064835	H1-hESC	embryonic stem cell:	n/a	chr12:9064295-9064309 chr12:9064296-9064310 chr12:9064631-9064645
8	POU5F1	chr12:9064259-9064874	H1-hESC	embryonic stem cell:	n/a	chr12:9064667-9064681 chr12:9064667-9064681 chr12:9064326-9064340 chr12:9064326-9064340 chr12:9064326-9064334
9	POLR2A	chr12:9064164-9064770	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr12:9064278-9064825	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr12:9064360-9064755	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr12:9064142-9064875	H1-hESC	embryonic stem cell:	n/a	chr12:9064377-9064386
13	E2F4	chr12:9064308-9064446	MCF10A-Er-Src	breast:	n/a	n/a
14	SIN3A	chr12:9064234-9069882	H1-hESC	embryonic stem cell:	n/a	chr12:9066956-9066965 chr12:9068258-9068267
15	ATF2	chr12:9064070-9064896	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr12:9064155-9065010	H1-hESC	embryonic stem cell:	n/a	n/a
17	SP1	chr12:9064169-9064918	H1-hESC	embryonic stem cell:	n/a	n/a
18	NANOG	chr12:9064217-9064889	H1-hESC	embryonic stem cell:	n/a	chr12:9064326-9064335
19	TEAD4	chr12:9064119-9064895	H1-hESC	embryonic stem cell:	n/a	chr12:9064377-9064386
20	MAFK	chr12:9064255-9064950	H1-hESC	embryonic stem cell:	n/a	n/a
21	CEBPB	chr12:9063883-9064778	H1-hESC	embryonic stem cell:	n/a	chr12:9064472-9064485 chr12:9064051-9064060 chr12:9064051-9064060 chr12:9064050-9064061
22	BACH1	chr12:9064191-9065063	H1-hESC	embryonic stem cell:	n/a	n/a
23	JUN	chr12:9064144-9064827	H1-hESC	embryonic stem cell:	n/a	chr12:9064292-9064301
24	CHD1	chr12:9063586-9066984	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr12:9063955-9067842	H1-hESC	embryonic stem cell:	n/a	n/a
26	YY1	chr12:9064177-9064857	H1-hESC	embryonic stem cell:	n/a	n/a
27	CEBPB	chr12:9063936-9064518	IMR90	lung:	n/a	chr12:9064472-9064485 chr12:9064051-9064060 chr12:9064051-9064060 chr12:9064050-9064061

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9064351..9068260-chr12:9100706..9102986,3	MCF-7	breast:
2	chr12:9062610..9065095-chr12:9066139..9068136,2	MCF-7	breast:

Variant related genes	Relation type
PHC1	TF binding region
ENSG00000003056	Chromatin interaction
ENSG00000111752	Chromatin interaction
ENSG00000139187	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10771185	0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs11611936	0.89[ASN][1000 genomes]
rs11612098	0.92[ASN][1000 genomes]
rs1805742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1805743	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883201	0.90[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs6487463	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs7295943	0.89[ASN][1000 genomes]
rs7297711	0.90[ASN][1000 genomes]
rs7302969	0.91[ASN][1000 genomes]
rs7306169	0.92[ASN][1000 genomes]
rs7959846	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1000824	MANSC1	cis	cerebellum	SCAN
rs1000824	PRB4	cis	cerebellum	SCAN
rs1000824	M6PR	cis	lung	GTEx
rs1000824	KLRB1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9050800-9065600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:9058800-9065400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:9059800-9065200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:9060000-9064600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:9060400-9065600	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:9060400-9065600	Weak transcription	Fetal Thymus	thymus
7	chr12:9060400-9066000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:9060600-9065600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:9062000-9064600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:9062400-9065600	Enhancers	Fetal Heart	heart
11	chr12:9062600-9066000	Weak transcription	Right Ventricle	heart
12	chr12:9062800-9064400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:9063000-9064400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:9063400-9064600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr12:9063600-9064600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:9063600-9064600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr12:9063600-9065600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:9063600-9066400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr12:9063800-9064600	Enhancers	Primary hematopoietic stem cells	blood
20	chr12:9063800-9064800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:9063800-9065200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:9063800-9069600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr12:9064000-9064600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr12:9064000-9065600	Enhancers	Fetal Lung	lung
25	chr12:9064200-9064400	Enhancers	Fetal Intestine Large	intestine
26	chr12:9064200-9064400	Enhancers	Fetal Kidney	kidney
27	chr12:9064200-9064600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
28	chr12:9064200-9064600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr12:9064200-9064600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr12:9064200-9064800	Enhancers	Primary B cells from peripheral blood	blood
31	chr12:9064200-9065400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:9064200-9065600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:9064200-9065800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:9064200-9065800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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