Variant report

Variant	rs11558768
Chromosome Location	chr12:48577789-48577790
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	CREB1	chr12:48576749-48577802	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3A	chr12:48576618-48579251	H1-hESC	embryonic stem cell:	n/a	chr12:48577451-48577460
3	MAX	chr12:48576656-48577909	A549	lung:	n/a	chr12:48577349-48577358 chr12:48577345-48577354
4	HDAC2	chr12:48576728-48577846	MCF-7	breast:	n/a	chr12:48577529-48577538
5	MXI1	chr12:48576436-48579525	SK-N-SH	brain:	n/a	chr12:48577343-48577358 chr12:48577345-48577360 chr12:48577379-48577394 chr12:48577381-48577396
6	RFX5	chr12:48575846-48577828	SK-N-SH	brain:	n/a	chr12:48577379-48577396 chr12:48577380-48577395 chr12:48577344-48577359 chr12:48577343-48577360 chr12:48577344-48577359 chr12:48577341-48577356 chr12:48577380-48577395 chr12:48577344-48577359 chr12:48577380-48577395
7	REST	chr12:48576228-48580563	H1-neurons	neurons:	n/a	chr12:48577348-48577357 chr12:48576911-48576924
8	MAX	chr12:48576748-48577839	A549	lung:	n/a	chr12:48577349-48577358 chr12:48577345-48577354
9	POLR2A	chr12:48576743-48578314	H1-neurons	neurons:	n/a	n/a
10	TAF1	chr12:48576665-48577843	H1-neurons	neurons:	n/a	n/a
11	ZBTB7A	chr12:48577039-48577910	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr12:48576750-48577813	SK-N-SH	brain:	n/a	chr12:48577349-48577358 chr12:48577345-48577354
13	CTCF	chr12:48576485-48578340	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr12:48577403-48577843	K562	blood:	n/a	n/a
15	CTBP2	chr12:48576803-48578719	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr12:48576494-48578211	A549	lung:	n/a	n/a
17	CTCF	chr12:48577780-48577930	SK-N-SH_RA	brain:	n/a	n/a
18	POLR2A	chr12:48576694-48580496	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48548408..48551386-chr12:48576630..48579457,3	K562	blood:
2	chr12:48576960..48580173-chr12:48592129..48594089,3	MCF-7	breast:
3	chr12:48549998..48552316-chr12:48577251..48580205,2	MCF-7	breast:

Variant related genes	Relation type
ASB8	TF binding region
ENSG00000177981	Chromatin interaction
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1021313	0.85[ASN][1000 genomes]
rs10219623	0.84[ASN][1000 genomes]
rs10437919	0.85[ASN][1000 genomes]
rs10437920	0.85[ASN][1000 genomes]
rs10467101	0.87[ASN][1000 genomes]
rs10783234	0.90[ASN][1000 genomes]
rs10875745	0.82[ASN][1000 genomes]
rs10875746	0.80[ASN][1000 genomes]
rs10875747	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875748	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875750	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10875756	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875762	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875764	0.91[ASN][1000 genomes]
rs10875767	0.89[ASN][1000 genomes]
rs10875768	0.87[ASN][1000 genomes]
rs10875769	0.82[ASN][1000 genomes]
rs10875770	0.89[ASN][1000 genomes]
rs10875772	0.87[ASN][1000 genomes]
rs10875777	0.85[ASN][1000 genomes]
rs10875778	0.85[ASN][1000 genomes]
rs10875779	0.85[ASN][1000 genomes]
rs10875782	0.82[ASN][1000 genomes]
rs11168413	0.82[ASN][1000 genomes]
rs11168414	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168418	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168420	0.82[EUR][1000 genomes]
rs11168422	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168425	0.81[ASN][1000 genomes]
rs11168427	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168433	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168450	0.91[ASN][1000 genomes]
rs11168459	0.89[ASN][1000 genomes]
rs11168483	0.82[ASN][1000 genomes]
rs11168487	0.85[ASN][1000 genomes]
rs11168508	0.81[ASN][1000 genomes]
rs12227601	0.81[ASN][1000 genomes]
rs12297470	0.84[ASN][1000 genomes]
rs12300647	0.82[ASN][1000 genomes]
rs12305511	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12305647	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12310813	0.84[ASN][1000 genomes]
rs12312134	0.92[ASN][1000 genomes]
rs12317751	0.85[ASN][1000 genomes]
rs12318705	0.82[ASN][1000 genomes]
rs17122666	0.84[EUR][1000 genomes]
rs17122812	0.89[ASN][1000 genomes]
rs1859445	0.82[ASN][1000 genomes]
rs2012773	0.91[ASN][1000 genomes]
rs2107638	0.84[ASN][1000 genomes]
rs2171642	0.82[ASN][1000 genomes]
rs2228500	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2269935	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286021	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2898065	0.84[ASN][1000 genomes]
rs2898066	0.80[ASN][1000 genomes]
rs4760622	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760625	0.81[ASN][1000 genomes]
rs4760681	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760687	0.89[ASN][1000 genomes]
rs4760689	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760690	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760695	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760696	0.91[ASN][1000 genomes]
rs4760697	0.90[ASN][1000 genomes]
rs61940962	0.89[ASN][1000 genomes]
rs61941003	0.85[ASN][1000 genomes]
rs61941006	0.85[ASN][1000 genomes]
rs6580659	0.89[ASN][1000 genomes]
rs7135779	0.91[ASN][1000 genomes]
rs716553	0.85[ASN][1000 genomes]
rs725454	0.82[EUR][1000 genomes]
rs7297298	0.81[ASN][1000 genomes]
rs7302466	0.82[ASN][1000 genomes]
rs7303055	0.85[ASN][1000 genomes]
rs7485355	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7486008	0.85[ASN][1000 genomes]
rs7486424	0.89[ASN][1000 genomes]
rs7975956	0.82[ASN][1000 genomes]
rs8804	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11558768	RP1-228P16.1	cis	Thyroid	GTEx
rs11558768	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs11558768	RP1-228P16.1	cis	lung	GTEx
rs11558768	RP1-228P16.1	cis	Artery Tibial	GTEx
rs11558768	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11558768	RP1-228P16.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48576200-48578000	Active TSS	Brain Anterior Caudate	brain
2	chr12:48576200-48578000	Active TSS	Right Atrium	heart
3	chr12:48576200-48578200	Active TSS	Aorta	Aorta
4	chr12:48576200-48578600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:48576200-48578600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:48576200-48579000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:48576200-48579000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:48576400-48577800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr12:48576400-48577800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
10	chr12:48576400-48577800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
11	chr12:48576400-48577800	Active TSS	NHLF	lung
12	chr12:48576400-48577800	Bivalent/Poised TSS	Osteobl	bone
13	chr12:48576400-48578000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
14	chr12:48576400-48578800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr12:48576400-48578800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr12:48576600-48577800	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr12:48576600-48577800	Active TSS	Brain Hippocampus Middle	brain
18	chr12:48576600-48577800	Bivalent/Poised TSS	Fetal Kidney	kidney
19	chr12:48576600-48577800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
20	chr12:48576600-48577800	Flanking Active TSS	Right Ventricle	heart
21	chr12:48576600-48577800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
22	chr12:48576600-48578000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:48576600-48578000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:48576600-48578000	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr12:48576600-48578000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:48576600-48578000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:48576600-48578000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:48576600-48578000	Active TSS	Brain Angular Gyrus	brain
29	chr12:48576600-48578200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:48576600-48578400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
31	chr12:48576600-48578400	Bivalent/Poised TSS	Thymus	Thymus
32	chr12:48576600-48578600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr12:48576600-48578600	Bivalent/Poised TSS	HSMM	muscle
34	chr12:48576600-48578800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
35	chr12:48576600-48579000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr12:48576600-48579000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:48576600-48579000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr12:48576600-48580400	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr12:48576800-48577800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:48576800-48577800	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:48576800-48577800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
42	chr12:48576800-48577800	Active TSS	Gastric	stomach
43	chr12:48576800-48577800	Active TSS	NH-A	brain
44	chr12:48576800-48578000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
45	chr12:48576800-48578000	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr12:48576800-48578000	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr12:48576800-48578000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr12:48576800-48578000	Active TSS	Brain Cingulate Gyrus	brain
49	chr12:48576800-48578000	Active TSS	Brain Substantia Nigra	brain
50	chr12:48576800-48578000	Active TSS	Fetal Brain Female	brain

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