Variant report

Variant	rs9425309
Chromosome Location	chr1:172386690-172386691
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	CEBPB	chr1:172386659-172387251	ECC-1	luminal epithelium:	n/a	chr1:172386992-172387003 chr1:172386992-172387005
2	TEAD4	chr1:172386547-172387255	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr1:172386456-172387183	ECC-1	luminal epithelium:	n/a	n/a
4	FOXA1	chr1:172386621-172387044	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr1:172386546-172387319	ECC-1	luminal epithelium:	n/a	chr1:172386605-172386619 chr1:172386993-172387007
6	TEAD4	chr1:172386590-172387173	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr1:172386484-172387188	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:172385755..172389106-chr1:172391207..172393719,3	K562	blood:
2	chr1:172370747..172372510-chr1:172384588..172387579,2	K562	blood:
3	chr1:172379952..172381876-chr1:172385382..172387129,2	MCF-7	breast:
4	chr1:172375496..172379926-chr1:172385834..172389157,4	MCF-7	breast:

Variant related genes	Relation type
C1orf105	TF binding region
PIGC	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10489286	1.00[ASN][1000 genomes]
rs1052256	1.00[ASN][1000 genomes]
rs10752953	1.00[ASN][1000 genomes]
rs1132148	1.00[ASN][1000 genomes]
rs12031216	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17277932	1.00[ASN][1000 genomes]
rs17369011	1.00[ASN][1000 genomes]
rs2422139	1.00[ASN][1000 genomes]
rs4916185	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916255	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916256	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56259646	1.00[ASN][1000 genomes]
rs56340136	1.00[ASN][1000 genomes]
rs61806074	1.00[ASN][1000 genomes]
rs61806089	1.00[ASN][1000 genomes]
rs61806090	1.00[ASN][1000 genomes]
rs61806091	1.00[ASN][1000 genomes]
rs6660051	1.00[ASN][1000 genomes]
rs6674018	1.00[ASN][1000 genomes]
rs9425307	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425308	1.00[YRI][hapmap]
rs9425314	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9425315	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9425606	1.00[YRI][hapmap]
rs9425610	1.00[ASN][1000 genomes]
rs978875	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172368400-172390800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:172373000-172390800	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:172373000-172390800	Weak transcription	Brain Substantia Nigra	brain
4	chr1:172373000-172411800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:172382200-172390800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:172383000-172387600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:172383000-172388600	Enhancers	NHEK	skin
8	chr1:172383400-172387600	Enhancers	HMEC	breast
9	chr1:172383800-172387200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:172384400-172398400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:172385000-172386800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:172385000-172391600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:172385400-172387400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr1:172385400-172387600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:172385400-172388000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:172385600-172386800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:172385600-172387400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:172385600-172387400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:172385800-172391000	Weak transcription	Fetal Lung	lung
20	chr1:172385800-172411000	Weak transcription	Fetal Stomach	stomach
21	chr1:172386000-172387200	Weak transcription	Primary T cells from cord blood	blood
22	chr1:172386000-172391200	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:172386400-172386800	Enhancers	Psoas Muscle	Psoas
24	chr1:172386400-172387400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:172386400-172387600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:172386600-172386800	Enhancers	Fetal Kidney	kidney
27	chr1:172386600-172386800	Enhancers	Fetal Thymus	thymus
28	chr1:172386600-172387000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:172386600-172387200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:172386600-172387200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:172386600-172387200	Enhancers	NH-A	brain
32	chr1:172386600-172387400	Enhancers	H1 Cell Line	embryonic stem cell

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