Variant report

Variant	rs2583236
Chromosome Location	chr12:104278375-104278376
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	RAD21	chr12:104277613-104278976	SK-N-SH	brain:	n/a	n/a
2	SPI1	chr12:104277900-104278752	GM12878	blood:	n/a	chr12:104278241-104278254 chr12:104278244-104278253
3	RAD21	chr12:104277921-104278462	A549	lung:	n/a	n/a
4	CTCF	chr12:104277847-104278936	A549	lung:	n/a	chr12:104278381-104278394 chr12:104278195-104278211
5	SPI1	chr12:104278142-104278485	HL-60	blood:	n/a	chr12:104278241-104278254 chr12:104278244-104278253
6	CTCF	chr12:104278017-104278412	IMR90	lung:	n/a	chr12:104278381-104278394 chr12:104278195-104278211
7	SPI1	chr12:104277965-104278520	HL-60	blood:	n/a	chr12:104278241-104278254 chr12:104278244-104278253
8	CTCF	chr12:104277996-104278414	GM12878	blood:	n/a	chr12:104278381-104278394 chr12:104278195-104278211
9	RAD21	chr12:104278057-104278431	HepG2	liver:	n/a	n/a
10	SPI1	chr12:104278018-104278500	GM12891	blood:	n/a	chr12:104278241-104278254 chr12:104278244-104278253
11	CTCF	chr12:104277939-104278443	MCF-7	breast:	n/a	chr12:104278381-104278394 chr12:104278195-104278211
12	RAD21	chr12:104278052-104278384	K562	blood:	n/a	n/a
13	RAD21	chr12:104278068-104278381	HepG2	liver:	n/a	n/a
14	RAD21	chr12:104278020-104278432	IMR90	lung:	n/a	n/a
15	RAD21	chr12:104278028-104278396	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr12:104277906-104278657	SK-N-SH	brain:	n/a	chr12:104278381-104278394 chr12:104278195-104278211
17	RAD21	chr12:104278016-104278465	A549	lung:	n/a	n/a
18	CTCF	chr12:104278006-104278389	K562	blood:	n/a	chr12:104278195-104278211
19	CTCF	chr12:104277950-104278389	MCF-7	breast:	n/a	chr12:104278195-104278211
20	RAD21	chr12:104277887-104278558	HCT-116	colon:	n/a	n/a
21	ZNF143	chr12:104278046-104278394	GM12878	blood:	n/a	n/a
22	RAD21	chr12:104278051-104278526	SK-N-SH_RA	brain:	n/a	n/a
23	RAD21	chr12:104278054-104278390	A549	lung:	n/a	n/a
24	CTCF	chr12:104278240-104278390	HFF-Myc	foreskin:	n/a	n/a
25	SPI1	chr12:104278087-104278401	GM12878	blood:	n/a	chr12:104278241-104278254 chr12:104278244-104278253
26	EP300	chr12:104278063-104278509	SK-N-SH_RA	brain:	n/a	chr12:104278165-104278179
27	CTCF	chr12:104278023-104278490	HCT-116	colon:	n/a	chr12:104278381-104278394 chr12:104278195-104278211
28	SMC3	chr12:104278027-104278496	GM12878	blood:	n/a	n/a
29	MAZ	chr12:104278095-104278378	K562	blood:	n/a	n/a
30	CTCF	chr12:104278012-104278395	A549	lung:	n/a	chr12:104278381-104278394 chr12:104278195-104278211
31	RAD21	chr12:104278031-104278408	HepG2	liver:	n/a	n/a
32	RAD21	chr12:104278011-104278612	GM12878	blood:	n/a	n/a
33	CTCF	chr12:104278072-104278400	A549	lung:	n/a	chr12:104278381-104278394 chr12:104278195-104278211
34	RAD21	chr12:104278044-104278457	ECC-1	luminal epithelium:	n/a	n/a
35	RAD21	chr12:104277917-104278509	MCF-7	breast:	n/a	n/a
36	RAD21	chr12:104278036-104278526	SK-N-SH_RA	brain:	n/a	n/a
37	RAD21	chr12:104278044-104278454	MCF-7	breast:	n/a	n/a
38	SPI1	chr12:104278023-104278446	GM12891	blood:	n/a	chr12:104278241-104278254 chr12:104278244-104278253
39	MXI1	chr12:104277868-104279101	SK-N-SH	brain:	n/a	n/a
40	RAD21	chr12:104277929-104278496	HCT-116	colon:	n/a	n/a
41	CTCF	chr12:104278300-104278450	GM12870	blood:	n/a	chr12:104278381-104278394
42	RAD21	chr12:104278029-104278403	Hela-S3	cervix:	n/a	n/a
43	FOXM1	chr12:104278035-104278430	GM12878	blood:	n/a	n/a
44	SMC3	chr12:104277841-104278611	SK-N-SH	brain:	n/a	n/a
45	RAD21	chr12:104277980-104278429	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104233142..104235484-chr12:104276450..104278828,3	K562	blood:
2	chr12:104276117..104279238-chr12:104322705..104326968,4	K562	blood:
3	chr12:103968788..103969666-chr12:104278125..104278702,2	MCF-7	breast:
4	chr12:104277824..104279928-chr12:104282058..104285020,2	K562	blood:
5	chr12:104277028..104280742-chr12:104283520..104285730,3	K562	blood:
6	chr12:104262529..104265193-chr12:104278298..104280290,2	K562	blood:
7	chr12:104276555..104279337-chr12:104325468..104328815,4	K562	blood:
8	chr12:104233142..104235198-chr12:104276474..104278828,2	K562	blood:
9	chr12:104277459..104278614-chr12:104502651..104503606,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214198	TF binding region
ENSG00000166598	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs1000295	0.89[JPT][hapmap]
rs10745982	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10745983	0.94[ASN][1000 genomes]
rs10745986	0.98[ASN][1000 genomes]
rs10745987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10745988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10745989	0.89[ASN][1000 genomes]
rs10745990	0.92[ASN][1000 genomes]
rs10778291	0.96[ASN][1000 genomes]
rs10778293	0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10778294	0.94[ASN][1000 genomes]
rs10778295	0.88[ASN][1000 genomes]
rs10778297	0.98[ASN][1000 genomes]
rs10778298	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10778299	0.98[ASN][1000 genomes]
rs10778300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10778301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10778302	0.97[ASN][1000 genomes]
rs10778303	0.98[ASN][1000 genomes]
rs10778304	0.98[ASN][1000 genomes]
rs10861126	0.94[ASN][1000 genomes]
rs10861128	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10861129	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10861134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10861135	0.98[ASN][1000 genomes]
rs10861136	0.86[ASN][1000 genomes]
rs10861137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10861138	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10861139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10861140	0.98[ASN][1000 genomes]
rs11111822	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11111823	0.98[ASN][1000 genomes]
rs11111824	0.98[ASN][1000 genomes]
rs11111827	0.94[ASN][1000 genomes]
rs11111828	0.85[ASN][1000 genomes]
rs11613427	0.98[ASN][1000 genomes]
rs1165596	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1165597	0.95[ASN][1000 genomes]
rs1165598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1185985	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12312978	0.96[ASN][1000 genomes]
rs1583599	0.94[ASN][1000 genomes]
rs1595338	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1595339	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2033730	0.99[ASN][1000 genomes]
rs2118313	0.89[JPT][hapmap]
rs2196614	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2248382	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2374350	0.94[ASN][1000 genomes]
rs2374351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2374352	0.92[ASN][1000 genomes]
rs2374353	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2439622	0.99[ASN][1000 genomes]
rs2576950	0.93[ASN][1000 genomes]
rs2576957	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2576958	0.97[ASN][1000 genomes]
rs2576960	0.99[ASN][1000 genomes]
rs2576961	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2576962	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2576963	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2576964	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs2576965	0.95[ASN][1000 genomes]
rs2576967	0.99[ASN][1000 genomes]
rs2576970	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2583240	0.95[ASN][1000 genomes]
rs2583241	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2583242	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2583243	0.94[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs2583245	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2583246	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2583247	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2583248	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2583249	0.87[ASN][1000 genomes]
rs2583250	0.85[ASN][1000 genomes]
rs2888809	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2888810	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34978042	0.86[ASN][1000 genomes]
rs3850016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3850017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3850018	0.98[ASN][1000 genomes]
rs3850019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3850020	0.94[ASN][1000 genomes]
rs4316574	0.94[ASN][1000 genomes]
rs4488278	0.94[ASN][1000 genomes]
rs4491322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4511355	0.98[ASN][1000 genomes]
rs4556622	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4964118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4964308	0.98[ASN][1000 genomes]
rs4964322	0.98[ASN][1000 genomes]
rs4964323	0.98[ASN][1000 genomes]
rs4964326	0.97[ASN][1000 genomes]
rs4964327	0.98[ASN][1000 genomes]
rs4964328	0.98[ASN][1000 genomes]
rs4964329	0.98[ASN][1000 genomes]
rs4964330	0.98[ASN][1000 genomes]
rs56205268	0.82[ASN][1000 genomes]
rs6539109	0.91[ASN][1000 genomes]
rs6539110	0.98[ASN][1000 genomes]
rs7136272	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7136297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7138145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7138345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7138361	0.98[ASN][1000 genomes]
rs728165	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs728166	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7294443	0.94[ASN][1000 genomes]
rs7295172	0.94[ASN][1000 genomes]
rs7295268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7295285	0.94[ASN][1000 genomes]
rs7295499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7295782	0.82[ASN][1000 genomes]
rs7298496	0.98[ASN][1000 genomes]
rs7298653	0.98[ASN][1000 genomes]
rs7298655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7299349	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7301439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7310988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7311473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7312936	0.93[ASN][1000 genomes]
rs7314790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs73175882	0.82[ASN][1000 genomes]
rs7488952	0.92[ASN][1000 genomes]
rs7956005	0.98[ASN][1000 genomes]
rs7956297	0.98[ASN][1000 genomes]
rs7957862	0.98[ASN][1000 genomes]
rs7963412	0.98[ASN][1000 genomes]
rs7964542	0.94[ASN][1000 genomes]
rs7964654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7967501	0.96[ASN][1000 genomes]
rs7970923	0.97[ASN][1000 genomes]
rs7971070	0.93[ASN][1000 genomes]
rs7971105	0.98[ASN][1000 genomes]
rs7979423	0.92[ASN][1000 genomes]
rs7979749	0.84[ASN][1000 genomes]
rs878125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs878126	0.99[ASN][1000 genomes]
rs9888379	0.94[ASN][1000 genomes]
rs9943750	0.86[ASN][1000 genomes]
rs9943761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9943762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9943812	0.98[ASN][1000 genomes]
rs9943844	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9988931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv977145	chr12:104273790-104283207	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2583236	LOC253724	cis	brain	BrainEAC

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104275000-104281600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:104276800-104278800	Enhancers	GM12878-XiMat	blood
3	chr12:104277400-104278400	Enhancers	Primary hematopoietic stem cells	blood
4	chr12:104277600-104278400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:104278000-104278400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:104278200-104278400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:104278200-104278600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr12:104278200-104278600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr12:104278200-104278600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:104278200-104278600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:104278200-104278600	Enhancers	Aorta	Aorta
12	chr12:104278200-104279200	Enhancers	Thymus	Thymus
13	chr12:104278200-104285800	Enhancers	Fetal Thymus	thymus

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