Variant report

Variant	rs11168415
Chromosome Location	chr12:48512521-48512522
allele	A/C
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	MAFK	chr12:48512441-48514143	Hela-S3	cervix:	n/a	chr12:48513708-48513724 chr12:48513711-48513725
2	TBP	chr12:48512342-48513566	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAZ	chr12:48512366-48513603	K562	blood:	n/a	chr12:48513547-48513555
4	TBP	chr12:48512231-48514177	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:48512252-48512534	K562	blood:	n/a	n/a
6	GATA1	chr12:48511733-48512570	PBDE	blood:	n/a	n/a
7	POLR2A	chr12:48512225-48512534	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:48512281-48514029	Hela-S3	cervix:	n/a	n/a
9	MYC	chr12:48512435-48513773	K562	blood:	n/a	chr12:48513547-48513555
10	POLR2A	chr12:48512108-48513729	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr12:48512462-48513892	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr12:48512103-48514432	SK-N-SH	brain:	n/a	n/a
13	RCOR1	chr12:48512347-48513705	K562	blood:	n/a	n/a
14	GTF2F1	chr12:48512344-48512551	Hela-S3	cervix:	n/a	n/a
15	MAX	chr12:48512451-48514245	Hela-S3	cervix:	n/a	chr12:48513547-48513555
16	POLR2A	chr12:48512114-48513952	SK-N-MC	brain:	n/a	n/a
17	MXI1	chr12:48512308-48514215	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48497262..48501671-chr12:48511273..48513832,5	K562	blood:
2	chr12:48511519..48514886-chr12:48548320..48552889,5	K562	blood:
3	chr12:48496389..48500489-chr12:48511491..48515053,4	K562	blood:
4	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
5	chr12:48510785..48513717-chr12:48592045..48593630,2	K562	blood:
6	chr12:48511276..48513909-chr12:48515822..48517335,2	K562	blood:

Variant related genes	Relation type
PFKM	TF binding region
ENSG00000269514	Chromatin interaction
ENSG00000079387	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000177981	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	0.93[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	0.80[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]
rs11168416	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	0.93[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	0.91[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	0.98[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	0.93[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	0.92[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	0.98[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
rs11168415	RP1-228P16.1	cis	Thyroid	GTEx
rs11168415	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11168415	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48512000-48512600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:48512200-48512600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48512200-48512600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:48512200-48512600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:48512200-48512600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr12:48512200-48512600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr12:48512200-48512600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr12:48512200-48512600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr12:48512200-48512600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:48512200-48512600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
11	chr12:48512200-48512600	Enhancers	Colon Smooth Muscle	Colon
12	chr12:48512200-48512600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr12:48512200-48512600	Enhancers	Fetal Heart	heart
14	chr12:48512200-48512600	Enhancers	Fetal Lung	lung
15	chr12:48512200-48512600	Enhancers	Fetal Muscle Leg	muscle
16	chr12:48512200-48512600	Enhancers	Stomach Mucosa	stomach
17	chr12:48512200-48512800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:48512200-48512800	Flanking Active TSS	Hela-S3	cervix
19	chr12:48512200-48512800	Flanking Active TSS	K562	blood
20	chr12:48512400-48512600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr12:48512400-48512600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr12:48512400-48512600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:48512400-48512600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr12:48512400-48512600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:48512400-48512600	Enhancers	Primary hematopoietic stem cells	blood
26	chr12:48512400-48512600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:48512400-48512600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:48512400-48512600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr12:48512400-48512600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr12:48512400-48512600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:48512400-48512600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:48512400-48512600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr12:48512400-48512600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:48512400-48512600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:48512400-48512600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:48512400-48512600	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr12:48512400-48512600	Enhancers	Brain Hippocampus Middle	brain
38	chr12:48512400-48512600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:48512400-48512600	Flanking Active TSS	Fetal Intestine Large	intestine
40	chr12:48512400-48512600	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr12:48512400-48512600	Enhancers	Fetal Muscle Trunk	muscle
42	chr12:48512400-48512600	Enhancers	Fetal Stomach	stomach
43	chr12:48512400-48512600	Enhancers	Fetal Thymus	thymus
44	chr12:48512400-48512600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
45	chr12:48512400-48512600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr12:48512400-48512600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr12:48512400-48512600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:48512400-48512600	Enhancers	Thymus	Thymus
49	chr12:48512400-48512600	Enhancers	HMEC	breast
50	chr12:48512400-48512600	Enhancers	NHLF	lung

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