Variant report

Variant	rs2546107
Chromosome Location	chr5:112159470-112159471
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	ZNF217	chr5:112159200-112159778	MCF-7	breast:	n/a	n/a
2	GATA3	chr5:112158924-112159891	MCF-7	breast:	n/a	chr5:112159279-112159286 chr5:112159161-112159174
3	SIN3AK20	chr5:112159087-112159971	MCF-7	breast:	n/a	n/a
4	CEBPB	chr5:112159245-112160047	MCF-7	breast:	n/a	chr5:112159859-112159870
5	NR2F2	chr5:112159227-112159685	MCF-7	breast:	n/a	n/a
6	GATA3	chr5:112159311-112159727	MCF-7	breast:	n/a	n/a
7	HDAC2	chr5:112159248-112159835	MCF-7	breast:	n/a	n/a
8	GATA3	chr5:112159045-112159685	MCF-7	breast:	n/a	chr5:112159279-112159286 chr5:112159161-112159174
9	CEBPB	chr5:112159277-112159744	MCF-7	breast:	n/a	n/a
10	GATA3	chr5:112159353-112159638	T-47D	breast:	n/a	n/a
11	EP300	chr5:112159378-112159722	MCF-7	breast:	n/a	n/a
12	GATA3	chr5:112159109-112160027	MCF-7	breast:	n/a	chr5:112159279-112159286 chr5:112159161-112159174

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112157931..112160849-chr5:112162546..112165691,3	MCF-7	breast:
2	chr5:112156563..112159936-chr5:112161937..112165418,3	K562	blood:

Variant related genes	Relation type
APC	TF binding region
ENSG00000258864	TF binding region
ENSG00000134982	Chromatin interaction
ENSG00000258864	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10051624	0.81[AMR][1000 genomes]
rs10071425	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11241183	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11241184	0.82[AMR][1000 genomes]
rs11241185	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11749701	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12518091	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12656359	0.83[EUR][1000 genomes]
rs12658609	0.81[AMR][1000 genomes]
rs13156251	0.88[AFR][1000 genomes]
rs1914	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1966476	0.90[ASN][1000 genomes]
rs1974786	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2019720	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2229992	0.93[ASN][1000 genomes]
rs2251913	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2253987	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2289484	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2431239	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2431241	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2431512	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2431514	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2439589	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2464803	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2545155	0.84[AMR][1000 genomes]
rs2545158	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2546106	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2546108	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2546110	0.95[ASN][1000 genomes]
rs2546112	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2546117	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2707763	0.83[AMR][1000 genomes]
rs2707765	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28373740	0.83[AMR][1000 genomes]
rs28578275	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2901844	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs351772	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35414976	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs373059	0.81[AMR][1000 genomes]
rs382427	0.82[AMR][1000 genomes]
rs390092	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs395858	0.82[AMR][1000 genomes]
rs41116	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs414098	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs448162	0.83[ASN][1000 genomes]
rs448475	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs454886	0.86[ASN][1000 genomes]
rs458906	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs467033	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4705486	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4705559	0.82[AFR][1000 genomes]
rs4705573	0.82[AFR][1000 genomes]
rs4705608	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705610	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705624	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs511906	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs518013	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs548710	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs566419	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62364017	0.80[AMR][1000 genomes]
rs6594646	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6879057	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7704618	0.93[AFR][1000 genomes]
rs9326863	0.82[AFR][1000 genomes]
rs9647582	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9647583	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][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	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2546107	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
4	chr5:112129400-112163800	Weak transcription	Small Intestine	intestine
5	chr5:112129600-112163600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:112131800-112164000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:112133600-112160800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:112133600-112161400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:112134000-112162800	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:112136600-112176200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:112141400-112162400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:112143600-112159800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:112144200-112159800	Strong transcription	HSMM	muscle
17	chr5:112145400-112165600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:112146200-112165800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:112149000-112163600	Weak transcription	A549	lung
20	chr5:112149400-112176400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr5:112149800-112159800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr5:112149800-112166400	Strong transcription	Fetal Thymus	thymus
23	chr5:112150200-112161200	Strong transcription	Primary B cells from cord blood	blood
24	chr5:112150200-112162000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr5:112150200-112177800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:112150400-112166600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:112151400-112176400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr5:112152000-112164200	Weak transcription	HMEC	breast
29	chr5:112152000-112170400	Weak transcription	Brain Angular Gyrus	brain
30	chr5:112152000-112183800	Weak transcription	Gastric	stomach
31	chr5:112152200-112163600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:112152200-112172000	Weak transcription	NHLF	lung
33	chr5:112153200-112160000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:112153200-112169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:112153400-112161800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:112153400-112165800	Strong transcription	Liver	Liver
39	chr5:112154000-112175200	Weak transcription	Stomach Mucosa	stomach
40	chr5:112154400-112159600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:112154400-112159800	Strong transcription	Fetal Muscle Leg	muscle
42	chr5:112154400-112160000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:112154400-112179400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:112154600-112159600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:112154600-112159600	Strong transcription	Fetal Brain Female	brain
46	chr5:112154600-112159600	Strong transcription	Fetal Intestine Large	intestine
47	chr5:112154600-112159800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr5:112154600-112177800	Strong transcription	Primary T cells from cord blood	blood
49	chr5:112154800-112159600	Strong transcription	Brain Germinal Matrix	brain
50	chr5:112154800-112160200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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