Variant report

Variant	rs12754557
Chromosome Location	chr1:184559788-184559789
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	SIN3AK20	chr1:184559266-184560135	MCF-7	breast:	n/a	n/a
2	CEBPB	chr1:184559449-184559863	MCF-7	breast:	n/a	n/a
3	NR2F2	chr1:184559430-184560006	MCF-7	breast:	n/a	n/a
4	EP300	chr1:184559583-184559892	MCF-7	breast:	n/a	chr1:184559718-184559725
5	SIN3AK20	chr1:184559449-184560047	MCF-7	breast:	n/a	n/a
6	ELF1	chr1:184559380-184560035	MCF-7	breast:	n/a	n/a
7	HDAC2	chr1:184559463-184559923	MCF-7	breast:	n/a	n/a
8	GATA3	chr1:184559308-184560152	MCF-7	breast:	n/a	n/a
9	CEBPB	chr1:184559491-184559983	MCF-7	breast:	n/a	n/a
10	HDAC2	chr1:184559510-184559989	MCF-7	breast:	n/a	n/a
11	GATA3	chr1:184559395-184560009	MCF-7	breast:	n/a	n/a
12	FOXA1	chr1:184559612-184559835	T-47D	breast:	n/a	n/a
13	NR2F2	chr1:184559427-184559996	MCF-7	breast:	n/a	n/a
14	FOSL2	chr1:184559521-184559870	MCF-7	breast:	n/a	n/a
15	JUND	chr1:184559395-184559918	MCF-7	breast:	n/a	n/a
16	GATA3	chr1:184559621-184559893	T-47D	breast:	n/a	n/a
17	ZNF217	chr1:184559317-184559969	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
C1orf21	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12082456	1.00[ASN][1000 genomes]
rs12726204	1.00[ASN][1000 genomes]
rs12727991	1.00[ASN][1000 genomes]
rs12735278	1.00[ASN][1000 genomes]
rs12743066	1.00[ASN][1000 genomes]
rs12743488	1.00[ASN][1000 genomes]
rs12746499	1.00[ASN][1000 genomes]
rs12754494	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756319	1.00[ASN][1000 genomes]
rs13374609	1.00[ASN][1000 genomes]
rs1547608	1.00[ASN][1000 genomes]
rs1856561	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180075	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34072105	1.00[ASN][1000 genomes]
rs34312759	1.00[ASN][1000 genomes]
rs34418556	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34427261	1.00[ASN][1000 genomes]
rs34579903	1.00[ASN][1000 genomes]
rs34591137	1.00[ASN][1000 genomes]
rs34712320	1.00[ASN][1000 genomes]
rs34946851	1.00[ASN][1000 genomes]
rs34959231	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35021091	1.00[ASN][1000 genomes]
rs35040136	1.00[ASN][1000 genomes]
rs35350002	1.00[ASN][1000 genomes]
rs35414247	1.00[ASN][1000 genomes]
rs35430213	1.00[ASN][1000 genomes]
rs35901887	1.00[ASN][1000 genomes]
rs4466608	1.00[ASN][1000 genomes]
rs4650665	1.00[ASN][1000 genomes]
rs4650668	1.00[ASN][1000 genomes]
rs4650669	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651212	1.00[ASN][1000 genomes]
rs4651222	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57978136	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59079733	1.00[ASN][1000 genomes]
rs66916459	1.00[ASN][1000 genomes]
rs67811250	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68054616	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71634106	1.00[ASN][1000 genomes]
rs71634108	1.00[ASN][1000 genomes]
rs71634109	1.00[ASN][1000 genomes]
rs74131659	1.00[ASN][1000 genomes]
rs7531736	1.00[ASN][1000 genomes]
rs9425342	1.00[ASN][1000 genomes]
rs9970629	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12754557	C1orf125	cis	parietal	SCAN
rs12754557	CEP350	cis	parietal	SCAN
rs12754557	NCF2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184546200-184563800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:184546200-184566600	Weak transcription	Left Ventricle	heart
3	chr1:184547800-184580000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:184549400-184564600	Weak transcription	NHDF-Ad	bronchial
5	chr1:184553200-184566200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:184553200-184566600	Weak transcription	Fetal Stomach	stomach
7	chr1:184553600-184566200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:184553600-184566200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:184555400-184561800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:184556800-184559800	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:184556800-184559800	Enhancers	Small Intestine	intestine
12	chr1:184557000-184566400	Weak transcription	Psoas Muscle	Psoas
13	chr1:184557000-184566400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:184557200-184566400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:184557200-184574000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:184557200-184591600	Weak transcription	Aorta	Aorta
17	chr1:184557800-184559800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:184558000-184559800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr1:184558000-184560400	Enhancers	Stomach Mucosa	stomach
20	chr1:184558000-184560600	Enhancers	Fetal Intestine Large	intestine
21	chr1:184558000-184560600	Enhancers	Fetal Intestine Small	intestine
22	chr1:184558400-184560000	Enhancers	Placenta	Placenta
23	chr1:184558400-184561800	Weak transcription	A549	lung
24	chr1:184558600-184560200	Enhancers	Liver	Liver
25	chr1:184558600-184564600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:184558600-184564800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:184558600-184566400	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:184558600-184568000	Weak transcription	Pancreas	Pancrea
29	chr1:184558600-184572600	Weak transcription	Lung	lung
30	chr1:184558800-184566600	Weak transcription	Fetal Lung	lung
31	chr1:184559000-184559800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:184559000-184559800	Enhancers	NHEK	skin
33	chr1:184559000-184560000	Enhancers	HMEC	breast
34	chr1:184559000-184588400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:184559200-184562000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:184559200-184564400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:184559200-184564800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:184559200-184566600	Weak transcription	Right Ventricle	heart
39	chr1:184559200-184580400	Weak transcription	Adipose Nuclei	Adipose
40	chr1:184559400-184559800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:184559400-184559800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:184559400-184560000	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:184559400-184580400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:184559600-184559800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:184559600-184560400	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr1:184559600-184563600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:184559600-184564600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:184559600-184564800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:184559600-184565000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:184559600-184578000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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