Variant report

Variant	rs73282593
Chromosome Location	chr12:46782961-46782962
allele	C/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	NR3C1	chr12:46782830-46783372	A549	lung:	n/a	chr12:46783162-46783179 chr12:46783164-46783178 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783164-46783179 chr12:46783030-46783044 chr12:46783158-46783184
2	TCF12	chr12:46782253-46783655	SK-N-SH	brain:	n/a	n/a
3	EP300	chr12:46781506-46783301	GM12878	blood:	n/a	chr12:46782338-46782347 chr12:46782337-46782351 chr12:46782418-46782432
4	PBX3	chr12:46782298-46783459	SK-N-SH	brain:	n/a	chr12:46783059-46783068
5	GATA3	chr12:46782358-46783619	SK-N-SH	brain:	n/a	chr12:46783071-46783082 chr12:46783075-46783084
6	GATA3	chr12:46782284-46783380	T-47D	breast:	n/a	chr12:46783071-46783082 chr12:46783075-46783084 chr12:46782339-46782349
7	NR3C1	chr12:46782906-46783353	A549	lung:	n/a	chr12:46783162-46783179 chr12:46783164-46783178 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783164-46783179 chr12:46783030-46783044 chr12:46783158-46783184
8	GATA2	chr12:46782492-46783323	HUVEC	blood vessel:	n/a	chr12:46783071-46783082 chr12:46783075-46783084
9	FOXA1	chr12:46782801-46783282	T-47D	breast:	n/a	n/a
10	PBX3	chr12:46782304-46783517	SK-N-SH	brain:	n/a	chr12:46783059-46783068
11	NR3C1	chr12:46782801-46783351	A549	lung:	n/a	chr12:46783162-46783179 chr12:46783164-46783178 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783164-46783179 chr12:46783030-46783044 chr12:46783158-46783184
12	POLR2A	chr12:46780098-46783057	GM12891	blood:	n/a	n/a
13	MAX	chr12:46782811-46783185	GM12878	blood:	n/a	n/a
14	TEAD4	chr12:46782326-46783588	SK-N-SH	brain:	n/a	chr12:46783141-46783150
15	FOSL2	chr12:46782385-46783486	SK-N-SH	brain:	n/a	chr12:46783021-46783030
16	EP300	chr12:46782178-46783379	T-47D	breast:	n/a	chr12:46782338-46782347 chr12:46782337-46782351 chr12:46782418-46782432
17	FOXA1	chr12:46782774-46783301	A549	lung:	n/a	n/a
18	RUNX3	chr12:46781327-46783021	GM12878	blood:	n/a	n/a
19	EP300	chr12:46782236-46783578	SK-N-SH	brain:	n/a	chr12:46782338-46782347 chr12:46782337-46782351 chr12:46782418-46782432
20	FOS	chr12:46782460-46783262	HUVEC	blood vessel:	n/a	chr12:46783021-46783030
21	CEBPB	chr12:46782594-46783324	IMR90	lung:	n/a	chr12:46782844-46782856
22	WRNIP1	chr12:46782285-46783207	GM12878	blood:	n/a	n/a
23	NR3C1	chr12:46782808-46783441	A549	lung:	n/a	chr12:46783162-46783179 chr12:46783164-46783178 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783164-46783179 chr12:46783030-46783044 chr12:46783158-46783184
24	TEAD4	chr12:46782254-46783456	SK-N-SH	brain:	n/a	chr12:46783141-46783150
25	MAFK	chr12:46782480-46783295	IMR90	lung:	n/a	n/a
26	GATA3	chr12:46782239-46783582	SK-N-SH	brain:	n/a	chr12:46783071-46783082 chr12:46783075-46783084 chr12:46782339-46782349
27	NFIC	chr12:46782262-46783571	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr12:46782873-46783004	MCF10A-Er-Src	breast:	n/a	n/a
29	RXRA	chr12:46782905-46783569	SK-N-SH	brain:	n/a	n/a
30	TCF12	chr12:46782168-46783665	SK-N-SH	brain:	n/a	n/a
31	NR3C1	chr12:46782849-46783338	A549	lung:	n/a	chr12:46783162-46783179 chr12:46783164-46783178 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783164-46783179 chr12:46783030-46783044 chr12:46783158-46783184
32	POLR2A	chr12:46782950-46783350	SK-N-SH	brain:	n/a	n/a
33	FOXA1	chr12:46782804-46783395	A549	lung:	n/a	n/a
34	NR3C1	chr12:46782833-46783361	A549	lung:	n/a	chr12:46783162-46783179 chr12:46783164-46783178 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783158-46783184 chr12:46783164-46783179 chr12:46783030-46783044 chr12:46783158-46783184
35	NFYB	chr12:46782941-46783233	GM12878	blood:	n/a	chr12:46783057-46783071 chr12:46783058-46783071 chr12:46783059-46783069 chr12:46783060-46783072 chr12:46783056-46783071 chr12:46783056-46783071
36	NFIC	chr12:46779940-46783129	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:46782366-46783025	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46661608..46665145-chr12:46782795..46784493,3	MCF-7	breast:
2	chr12:46782810..46784901-chr12:46849696..46851269,2	MCF-7	breast:
3	chr12:46781039..46783581-chr12:46796813..46799166,3	K562	blood:
4	chr12:46781028..46783722-chr12:46834423..46837382,2	K562	blood:
5	chr12:46782004..46784906-chr12:46849046..46851285,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARID2-12	chr12:46782639-46785909	NONHSAT027878

Variant related genes	Relation type
ENSG00000257496	TF binding region
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11183453	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833812	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11834593	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1948425	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307059	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55795804	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57199226	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57786829	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58545634	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59546893	0.96[EUR][1000 genomes]
rs7953450	0.82[AFR][1000 genomes]
rs7967840	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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	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:107 , 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	chr12:46778400-46783400	Enhancers	Fetal Heart	heart
3	chr12:46778400-46784200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:46778400-46786800	Enhancers	NHDF-Ad	bronchial
5	chr12:46778600-46783600	Enhancers	HMEC	breast
6	chr12:46778600-46784200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr12:46778600-46785400	Enhancers	Adipose Nuclei	Adipose
8	chr12:46778600-46787000	Enhancers	Fetal Lung	lung
9	chr12:46778800-46784000	Enhancers	Duodenum Mucosa	Duodenum
10	chr12:46778800-46797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:46779200-46783400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:46779600-46783600	Enhancers	NH-A	brain
13	chr12:46779600-46786000	Weak transcription	Gastric	stomach
14	chr12:46779600-46786400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:46779600-46786400	Weak transcription	Right Ventricle	heart
16	chr12:46779600-46802800	Weak transcription	Pancreas	Pancrea
17	chr12:46780400-46783200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:46780400-46784400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:46780600-46783200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr12:46780600-46783200	Enhancers	Fetal Thymus	thymus
21	chr12:46780600-46783400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr12:46780600-46786800	Weak transcription	Brain Substantia Nigra	brain
23	chr12:46780600-46788600	Weak transcription	Fetal Brain Male	brain
24	chr12:46780800-46783000	Enhancers	Thymus	Thymus
25	chr12:46780800-46783000	Flanking Active TSS	Osteobl	bone
26	chr12:46780800-46784000	Weak transcription	Stomach Mucosa	stomach
27	chr12:46780800-46785600	Enhancers	Liver	Liver
28	chr12:46781000-46784400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:46781000-46784600	Weak transcription	Fetal Intestine Large	intestine
30	chr12:46781000-46785600	Flanking Active TSS	GM12878-XiMat	blood
31	chr12:46781200-46783000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:46781200-46783000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:46781200-46783200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:46781200-46785600	Enhancers	HUVEC	blood vessel
35	chr12:46781400-46783000	Enhancers	Primary hematopoietic stem cells	blood
36	chr12:46781400-46783000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:46781400-46783400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr12:46781400-46783400	Enhancers	HSMM	muscle
39	chr12:46781400-46783600	Enhancers	HSMMtube	muscle
40	chr12:46781400-46786600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:46781400-46787000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr12:46781400-46787200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:46781600-46783200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr12:46781600-46783400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:46781600-46783600	Genic enhancers	NHEK	skin
46	chr12:46781600-46783800	Weak transcription	Fetal Intestine Small	intestine
47	chr12:46781600-46784000	Enhancers	A549	lung
48	chr12:46781600-46789200	Weak transcription	Fetal Stomach	stomach
49	chr12:46781600-46795400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:46781800-46783200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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