Variant report

Variant	rs10735933
Chromosome Location	chr12:66459794-66459795
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	NFIC	chr12:66459422-66460940	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr12:66458556-66460648	SK-N-SH	brain:	n/a	n/a
3	SMC3	chr12:66459777-66461122	GM12878	blood:	n/a	n/a
4	PBX3	chr12:66459671-66460350	SK-N-SH	brain:	n/a	n/a
5	RUNX3	chr12:66459441-66460923	GM12878	blood:	n/a	n/a
6	TEAD4	chr12:66459741-66460744	ECC-1	luminal epithelium:	n/a	n/a
7	GATA3	chr12:66458797-66460570	SK-N-SH	brain:	n/a	chr12:66459273-66459294 chr12:66459411-66459428
8	NFIC	chr12:66458873-66460717	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr12:66459733-66460839	ECC-1	luminal epithelium:	n/a	n/a
10	IKZF1	chr12:66459654-66460866	GM12878	blood:	n/a	n/a
11	EP300	chr12:66459598-66460883	ECC-1	luminal epithelium:	n/a	chr12:66459697-66459711
12	TEAD4	chr12:66459761-66460860	ECC-1	luminal epithelium:	n/a	n/a
13	GATA3	chr12:66459709-66460581	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr12:66458709-66460620	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr12:66459339-66459801	SK-N-MC	brain:	n/a	n/a
16	EBF1	chr12:66459756-66460838	GM12878	blood:	n/a	n/a
17	NFIC	chr12:66459715-66460860	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
RNA5SP362	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10878381	0.81[CHB][hapmap]
rs10878382	0.81[CHB][hapmap]
rs10878383	0.86[CHB][hapmap]
rs10878389	0.81[CHB][hapmap]
rs11176043	0.81[CHB][hapmap]
rs11176056	0.81[CHB][hapmap]
rs11176082	0.82[JPT][hapmap]
rs12832926	0.81[CHB][hapmap]
rs17767200	0.81[CHB][hapmap]
rs1898304	0.85[CHB][hapmap]
rs2178486	0.81[CHB][hapmap]
rs2870781	0.86[CHB][hapmap]
rs34878787	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295147	0.81[CHB][hapmap]
rs7966561	0.81[CHB][hapmap]
rs7979029	0.81[CHB][hapmap]
rs9989009	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899213	chr12:66389968-66500036	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10735933	RP11-745O10.2	cis	Thyroid	GTEx
rs10735933	RP11-745O10.2	cis	Whole Blood	GTEx
rs10735933	IRAK3	Cis_1M	lymphoblastoid	RTeQTL
rs10735933	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs10735933	RP11-745O10.2	cis	lung	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66453800-66460800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:66455800-66461200	Enhancers	NHDF-Ad	bronchial
3	chr12:66456000-66460200	Weak transcription	Fetal Kidney	kidney
4	chr12:66457200-66460000	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:66457400-66459800	Weak transcription	Fetal Stomach	stomach
6	chr12:66457800-66461200	Enhancers	NHLF	lung
7	chr12:66458600-66460600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:66458800-66460400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:66458800-66460800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr12:66458800-66460800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:66458800-66460800	Enhancers	NH-A	brain
12	chr12:66458800-66461200	Enhancers	Primary hematopoietic stem cells	blood
13	chr12:66459000-66459800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:66459000-66460000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:66459000-66460000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:66459400-66459800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:66459400-66460000	Enhancers	GM12878-XiMat	blood
18	chr12:66459400-66460600	Enhancers	Fetal Lung	lung
19	chr12:66459400-66461000	Enhancers	Fetal Brain Male	brain
20	chr12:66459400-66461200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:66459400-66461600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:66459600-66459800	Flanking Active TSS	Osteobl	bone
23	chr12:66459600-66460000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:66459600-66460400	Enhancers	HepG2	liver
25	chr12:66459600-66460800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:66459600-66460800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:66459600-66461000	Enhancers	Fetal Brain Female	brain

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