Variant report

Variant	rs923788
Chromosome Location	chr12:46781442-46781443
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	RELA	chr12:46780274-46782562	GM19099	blood:	n/a	n/a
2	MAX	chr12:46780055-46781454	ECC-1	luminal epithelium:	n/a	n/a
3	RELA	chr12:46780469-46781812	GM19193	blood:	n/a	n/a
4	PML	chr12:46780131-46781875	GM12878	blood:	n/a	n/a
5	MAX	chr12:46780559-46781612	NB4	blood:	n/a	n/a
6	RELA	chr12:46780650-46781923	GM15510	blood:	n/a	n/a
7	FOXM1	chr12:46780638-46781799	GM12878	blood:	n/a	n/a
8	TBP	chr12:46781297-46781912	GM12878	blood:	n/a	n/a
9	JUND	chr12:46780040-46781457	T-47D	breast:	n/a	chr12:46780420-46780428 chr12:46780416-46780427 chr12:46780558-46780567
10	FOXA1	chr12:46781000-46781483	T-47D	breast:	n/a	n/a
11	USF1	chr12:46781024-46781452	ECC-1	luminal epithelium:	n/a	chr12:46781195-46781216
12	MTA3	chr12:46781300-46782676	GM12878	blood:	n/a	n/a
13	GATA3	chr12:46780947-46781478	T-47D	breast:	n/a	n/a
14	EBF1	chr12:46781431-46781788	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:46780119-46782654	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:46780098-46783057	GM12891	blood:	n/a	n/a
17	EBF1	chr12:46781400-46781855	GM12878	blood:	n/a	n/a
18	TFAP2C	chr12:46780733-46781763	Hela-S3	cervix:	n/a	chr12:46781247-46781262
19	RELA	chr12:46780380-46781866	GM12878	blood:	n/a	n/a
20	SMARCC1	chr12:46780297-46781874	Hela-S3	cervix:	n/a	n/a
21	RELA	chr12:46780650-46781960	GM18951	blood:	n/a	n/a
22	USF1	chr12:46780701-46781459	ECC-1	luminal epithelium:	n/a	chr12:46781195-46781216
23	RUNX3	chr12:46781327-46783021	GM12878	blood:	n/a	n/a
24	EBF1	chr12:46781315-46782627	GM12878	blood:	n/a	n/a
25	GATA3	chr12:46780975-46781449	T-47D	breast:	n/a	n/a
26	RELA	chr12:46780653-46781895	GM12891	blood:	n/a	n/a
27	CREB1	chr12:46780304-46782638	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:46780681-46781677	SK-N-MC	brain:	n/a	n/a
29	SMC3	chr12:46781312-46782499	GM12878	blood:	n/a	n/a
30	MAX	chr12:46780776-46781846	GM12878	blood:	n/a	n/a
31	EP300	chr12:46780763-46781587	T-47D	breast:	n/a	n/a
32	RCOR1	chr12:46780732-46781456	K562	blood:	n/a	n/a
33	RUNX3	chr12:46781390-46781978	GM12878	blood:	n/a	n/a
34	MAX	chr12:46780825-46781443	MCF-7	breast:	n/a	n/a
35	IKZF1	chr12:46780744-46781698	GM12878	blood:	n/a	n/a
36	TCF7L2	chr12:46780102-46781741	Hela-S3	cervix:	n/a	n/a
37	EP300	chr12:46780742-46781514	GM12878	blood:	n/a	n/a
38	NFIC	chr12:46780182-46781459	GM12878	blood:	n/a	n/a
39	BHLHE40	chr12:46780432-46781821	GM12878	blood:	n/a	chr12:46781195-46781216
40	TFAP2A	chr12:46780817-46781664	Hela-S3	cervix:	n/a	chr12:46781245-46781260
41	NFIC	chr12:46779940-46783129	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46781039..46783581-chr12:46796813..46799166,3	K562	blood:
2	chr12:46781028..46783722-chr12:46834423..46837382,2	K562	blood:

Variant related genes	Relation type
ENSG00000257496	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10506267	1.00[EUR][1000 genomes]
rs10506268	1.00[EUR][1000 genomes]
rs11183454	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11183467	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11183482	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11183487	1.00[AMR][1000 genomes]
rs1125908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11830769	1.00[EUR][1000 genomes]
rs11834905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299499	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12314541	0.81[YRI][hapmap]
rs12317255	1.00[AMR][1000 genomes]
rs12320438	1.00[AMR][1000 genomes]
rs12321512	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12321642	1.00[AMR][1000 genomes]
rs12322378	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13377959	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17096884	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17096896	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17096922	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2125646	1.00[EUR][1000 genomes]
rs2307062	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2307063	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2408509	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34280632	1.00[AMR][1000 genomes]
rs35875247	1.00[AMR][1000 genomes]
rs36010856	1.00[AMR][1000 genomes]
rs3742061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768118	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs56036156	1.00[AMR][1000 genomes]
rs56196954	1.00[AMR][1000 genomes]
rs56222195	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56314009	1.00[AMR][1000 genomes]
rs57067899	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57149475	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57271454	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57425661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58460251	1.00[AMR][1000 genomes]
rs58890669	1.00[AMR][1000 genomes]
rs59608605	1.00[AMR][1000 genomes]
rs60565802	1.00[AMR][1000 genomes]
rs60628240	1.00[EUR][1000 genomes]
rs60878594	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60977966	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61232019	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61406609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61517444	1.00[EUR][1000 genomes]
rs73282532	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73282561	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73282591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73290315	1.00[AMR][1000 genomes]
rs74082254	1.00[AMR][1000 genomes]
rs74083707	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74083710	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74084031	1.00[EUR][1000 genomes]
rs7488027	1.00[AMR][1000 genomes]
rs7954314	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7965618	1.00[AMR][1000 genomes]
rs7967889	0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs7977319	1.00[AMR][1000 genomes]
rs9669404	1.00[YRI][hapmap];0.83[AFR][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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46778200-46784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:46778400-46781600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:46778400-46781600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:46778400-46781600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:46778400-46781600	Weak transcription	Colonic Mucosa	Colon
6	chr12:46778400-46781600	Enhancers	Fetal Stomach	stomach
7	chr12:46778400-46782200	Enhancers	Colon Smooth Muscle	Colon
8	chr12:46778400-46782800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:46778400-46782800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr12:46778400-46783400	Enhancers	Fetal Heart	heart
11	chr12:46778400-46784200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:46778400-46786800	Enhancers	NHDF-Ad	bronchial
13	chr12:46778600-46781600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:46778600-46781800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:46778600-46782000	Enhancers	Fetal Kidney	kidney
16	chr12:46778600-46782400	Enhancers	Dnd41	blood
17	chr12:46778600-46783600	Enhancers	HMEC	breast
18	chr12:46778600-46784200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr12:46778600-46785400	Enhancers	Adipose Nuclei	Adipose
20	chr12:46778600-46787000	Enhancers	Fetal Lung	lung
21	chr12:46778800-46781600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:46778800-46784000	Enhancers	Duodenum Mucosa	Duodenum
23	chr12:46778800-46797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:46779200-46783400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:46779400-46782000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr12:46779400-46782800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:46779600-46781600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:46779600-46781600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:46779600-46782800	Weak transcription	Ovary	ovary
30	chr12:46779600-46783600	Enhancers	NH-A	brain
31	chr12:46779600-46786000	Weak transcription	Gastric	stomach
32	chr12:46779600-46786400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:46779600-46786400	Weak transcription	Right Ventricle	heart
34	chr12:46779600-46802800	Weak transcription	Pancreas	Pancrea
35	chr12:46780000-46781600	Flanking Active TSS	NHEK	skin
36	chr12:46780000-46782200	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr12:46780200-46781600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr12:46780200-46782400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr12:46780400-46782200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:46780400-46782200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:46780400-46783200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:46780400-46784400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:46780600-46782000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:46780600-46782200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr12:46780600-46782800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:46780600-46783200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr12:46780600-46783200	Enhancers	Fetal Thymus	thymus
48	chr12:46780600-46783400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr12:46780600-46786800	Weak transcription	Brain Substantia Nigra	brain
50	chr12:46780600-46788600	Weak transcription	Fetal Brain Male	brain

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