Variant report

Variant	rs11168416
Chromosome Location	chr12:48513979-48513980
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	POLR2A	chr12:48512741-48513993	MCF10A-Er-Src	breast:	n/a	n/a
2	MAFK	chr12:48512441-48514143	Hela-S3	cervix:	n/a	chr12:48513708-48513724 chr12:48513711-48513725
3	TBP	chr12:48512231-48514177	Hela-S3	cervix:	n/a	n/a
4	RFX5	chr12:48512629-48514275	Hela-S3	cervix:	n/a	chr12:48514134-48514142
5	MYC	chr12:48512913-48514155	MCF10A-Er-Src	breast:	n/a	chr12:48513547-48513555
6	POLR2A	chr12:48512281-48514029	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr12:48512723-48514384	Hela-S3	cervix:	n/a	n/a
8	MYC	chr12:48512859-48514318	MCF10A-Er-Src	breast:	n/a	chr12:48513547-48513555
9	MXI1	chr12:48512103-48514432	SK-N-SH	brain:	n/a	n/a
10	MAX	chr12:48512451-48514245	Hela-S3	cervix:	n/a	chr12:48513547-48513555
11	REST	chr12:48512573-48514094	H1-neurons	neurons:	n/a	chr12:48513389-48513402 chr12:48513360-48513380
12	MXI1	chr12:48512308-48514215	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48511519..48514886-chr12:48548320..48552889,5	K562	blood:
2	chr12:48496389..48500489-chr12:48511491..48515053,4	K562	blood:
3	chr12:48498567..48501846-chr12:48512929..48518601,8	MCF-7	breast:
4	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
5	chr12:48513033..48514796-chr12:48515513..48517416,2	MCF-7	breast:

Variant related genes	Relation type
PFKM	TF binding region
ENSG00000177981	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10082861	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10219623	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10219645	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875745	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875746	0.95[ASN][1000 genomes]
rs10875747	0.97[ASN][1000 genomes]
rs10875748	0.97[ASN][1000 genomes]
rs10875750	0.95[ASN][1000 genomes]
rs10875756	0.87[ASN][1000 genomes]
rs11168413	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168414	0.97[ASN][1000 genomes]
rs11168415	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168418	0.97[ASN][1000 genomes]
rs11168420	0.90[ASN][1000 genomes]
rs11168421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168422	0.97[ASN][1000 genomes]
rs11168425	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168427	0.94[ASN][1000 genomes]
rs11168433	0.87[ASN][1000 genomes]
rs12297470	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12306290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12310813	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12312134	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17122666	0.91[ASN][1000 genomes]
rs1859445	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107638	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228500	0.97[ASN][1000 genomes]
rs2269933	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269935	0.97[ASN][1000 genomes]
rs2286021	0.95[ASN][1000 genomes]
rs4760619	0.90[ASN][1000 genomes]
rs4760681	0.95[ASN][1000 genomes]
rs4760684	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760687	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760689	0.87[ASN][1000 genomes]
rs4760690	0.87[ASN][1000 genomes]
rs60106007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61343568	0.94[ASN][1000 genomes]
rs725454	0.91[ASN][1000 genomes]
rs7485355	0.95[ASN][1000 genomes]
rs7486424	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8804	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11168416	RP1-228P16.1	cis	Artery Tibial	GTEx
rs11168416	RP1-228P16.1	cis	Thyroid	GTEx
rs11168416	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48512400-48514000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:48512400-48514000	Active TSS	Brain Anterior Caudate	brain
3	chr12:48512400-48514200	Active TSS	Ovary	ovary
4	chr12:48512400-48514400	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:48512400-48514600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:48512400-48514800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:48512400-48515400	Active TSS	Brain Angular Gyrus	brain
8	chr12:48512600-48514000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:48512600-48514000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:48512600-48514000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:48512600-48514000	Active TSS	Brain Germinal Matrix	brain
12	chr12:48512600-48514000	Active TSS	Fetal Intestine Large	intestine
13	chr12:48512600-48514000	Active TSS	Fetal Kidney	kidney
14	chr12:48512600-48514000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr12:48512600-48514000	Active TSS	Placenta	Placenta
16	chr12:48512600-48514200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr12:48512600-48514200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr12:48512600-48514200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:48512600-48514200	Active TSS	Brain Cingulate Gyrus	brain
20	chr12:48512600-48514200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:48512600-48514200	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr12:48512600-48514200	Active TSS	NHDF-Ad	bronchial
23	chr12:48512600-48514600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:48512600-48516400	Active TSS	Right Atrium	heart
25	chr12:48512800-48514000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr12:48512800-48514000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:48512800-48514000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr12:48512800-48514000	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr12:48512800-48514000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:48512800-48514000	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:48512800-48514000	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr12:48512800-48514000	Active TSS	Aorta	Aorta
33	chr12:48512800-48514000	Active TSS	Esophagus	oesophagus
34	chr12:48512800-48514200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:48512800-48514200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:48512800-48514200	Active TSS	HSMMtube	muscle
37	chr12:48512800-48514400	Active TSS	Muscle Satellite Cultured Cells	--
38	chr12:48512800-48514400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:48512800-48514400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:48512800-48514600	Active TSS	Psoas Muscle	Psoas
41	chr12:48512800-48514600	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr12:48512800-48514800	Active TSS	Brain Hippocampus Middle	brain
43	chr12:48512800-48515000	Active TSS	Right Ventricle	heart
44	chr12:48512800-48515200	Active TSS	Left Ventricle	heart
45	chr12:48512800-48515800	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr12:48513000-48514000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:48513000-48514000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:48513000-48514000	Active TSS	HMEC	breast
49	chr12:48513000-48514200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:48513000-48514200	Active TSS	Fetal Brain Male	brain

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