Variant report

Variant	rs12371487
Chromosome Location	chr12:63001009-63001010
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	POLR2A	chr12:62999540-63001041	SK-N-SH	brain:	n/a	n/a
2	FOXM1	chr12:63000642-63001104	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:62999257-63001028	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:62995037-63001628	GM12891	blood:	n/a	n/a
5	POLR2A	chr12:62995668-63001032	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:62995938-63002376	U87	brain:	n/a	n/a
7	POLR2A	chr12:62995424-63002267	U87	brain:	n/a	n/a
8	POLR2A	chr12:63000376-63001881	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:62995938-63002365	U87	brain:	n/a	n/a
10	PBX3	chr12:63000393-63001023	A549	lung:	n/a	n/a
11	TCF12	chr12:62995491-63001122	A549	lung:	n/a	n/a
12	ELF1	chr12:63000284-63001110	A549	lung:	n/a	n/a
13	MAX	chr12:62999754-63001116	A549	lung:	n/a	n/a
14	POLR2A	chr12:62995454-63001211	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr12:62995424-63002364	U87	brain:	n/a	n/a
16	NFIC	chr12:63000596-63001151	GM12878	blood:	n/a	n/a
17	ZBTB33	chr12:63000204-63001064	A549	lung:	n/a	n/a
18	RUNX3	chr12:63000389-63001119	GM12878	blood:	n/a	n/a
19	NFATC1	chr12:63000444-63001193	GM12878	blood:	n/a	n/a
20	BCL3	chr12:62999438-63001165	A549	lung:	n/a	n/a
21	POLR2A	chr12:62999829-63001065	HUVEC	blood vessel:	n/a	n/a
22	FOSL2	chr12:62999171-63001033	A549	lung:	n/a	chr12:63000121-63000130
23	POLR2A	chr12:62999765-63001059	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr12:62995208-63001924	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr12:62998759-63001578	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr12:62996032-63001077	A549	lung:	n/a	n/a
27	SP1	chr12:62999727-63001014	A549	lung:	n/a	n/a
28	PBX3	chr12:63000266-63001160	A549	lung:	n/a	n/a
29	POLR2A	chr12:62994755-63002267	GM12878	blood:	n/a	n/a
30	GATA3	chr12:62995840-63001125	A549	lung:	n/a	chr12:63001050-63001057 chr12:62998843-62998851 chr12:62998844-62998851 chr12:62997355-62997365 chr12:63001049-63001059 chr12:63001050-63001057 chr12:62998842-62998855 chr12:63001043-63001064 chr12:63001046-63001062 chr12:62999370-62999377 chr12:63001050-63001057
31	BCL3	chr12:62995675-63002413	A549	lung:	n/a	chr12:62997568-62997577 chr12:62997367-62997376
32	POLR2A	chr12:62995628-63002228	K562	blood:	n/a	n/a
33	POLR2A	chr12:62999552-63001097	GM12878	blood:	n/a	n/a
34	REST	chr12:62995843-63001063	A549	lung:	n/a	chr12:62997605-62997615 chr12:62997314-62997327

No.	Distal block	Cell Line	Cell type
1	chr12:63000207..63003968-chr12:63019804..63022918,4	MCF-7	breast:
2	chr12:63000399..63002714-chr12:63116327..63118895,2	MCF-7	breast:
3	chr12:62999244..63001612-chr12:63021259..63022888,2	K562	blood:
4	chr12:62999257..63001117-chr12:63014649..63017170,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MON2-2	chr12:62997216-63015942	NONHSAT029092

Variant related genes	Relation type
C12orf61	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11174492	1.00[EUR][1000 genomes]
rs11174499	1.00[EUR][1000 genomes]
rs11174500	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11174501	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11174506	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11174512	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11174524	1.00[EUR][1000 genomes]
rs11174548	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11174556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12368038	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163691	1.00[CHB][hapmap]
rs17718211	1.00[EUR][1000 genomes]
rs7137985	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7308812	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7309464	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7314752	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7964242	0.93[EUR][1000 genomes]
rs7966718	0.83[EUR][1000 genomes]
rs7970822	1.00[EUR][1000 genomes]
rs7976993	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62997800-63012800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:62997800-63019200	Weak transcription	Spleen	Spleen
3	chr12:62998000-63010200	Weak transcription	Lung	lung
4	chr12:62998000-63019200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:62998200-63001600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:62998800-63001200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:62998800-63012800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:62999000-63004600	Weak transcription	Left Ventricle	heart
9	chr12:62999000-63006800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:62999000-63019200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:62999200-63001400	Weak transcription	K562	blood
12	chr12:62999200-63002000	Weak transcription	HSMM	muscle
13	chr12:62999200-63005600	Weak transcription	Fetal Intestine Small	intestine
14	chr12:62999200-63012200	Weak transcription	Fetal Thymus	thymus
15	chr12:62999200-63013200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:62999400-63010800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:62999400-63012000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:62999400-63025000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:62999600-63001600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:62999600-63003200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:62999600-63011600	Weak transcription	Fetal Stomach	stomach
22	chr12:62999600-63012800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:62999800-63001800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:62999800-63004400	Weak transcription	HepG2	liver
25	chr12:62999800-63012600	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:62999800-63013400	Weak transcription	Primary B cells from cord blood	blood
27	chr12:63000000-63002600	Weak transcription	Right Atrium	heart
28	chr12:63000000-63009400	Weak transcription	HSMMtube	muscle
29	chr12:63000000-63012400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:63000000-63019000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:63000200-63001200	Enhancers	Brain Germinal Matrix	brain
32	chr12:63000200-63001400	Weak transcription	Right Ventricle	heart
33	chr12:63000200-63002600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:63000200-63004600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:63000200-63006200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:63000200-63012400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:63000200-63013000	Weak transcription	NHLF	lung
38	chr12:63000200-63015000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:63000200-63020600	Weak transcription	HMEC	breast
40	chr12:63000600-63001200	Enhancers	HUVEC	blood vessel
41	chr12:63000600-63003400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:63000600-63003400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:63000600-63003600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:63000600-63006000	Weak transcription	NHDF-Ad	bronchial
45	chr12:63000600-63009000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:63000600-63009200	Weak transcription	Psoas Muscle	Psoas
47	chr12:63000600-63019200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:63000800-63001200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:63000800-63001200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:63000800-63001200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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