Variant report

Variant	rs2258287
Chromosome Location	chr12:121454313-121454314
allele	G/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	MTA3	chr12:121453914-121454533	GM12878	blood:	n/a	n/a
2	NFYA	chr12:121454154-121454508	Hela-S3	cervix:	n/a	n/a
3	RUNX3	chr12:121453946-121454574	GM12878	blood:	n/a	n/a
4	YY1	chr12:121453837-121454704	GM12878	blood:	n/a	chr12:121454269-121454281
5	CREB1	chr12:121454019-121454685	GM12878	blood:	n/a	chr12:121454329-121454342
6	ATF3	chr12:121454171-121454453	K562	blood:	n/a	chr12:121454331-121454339 chr12:121454330-121454343 chr12:121454330-121454341 chr12:121454332-121454339 chr12:121454329-121454339 chr12:121454336-121454345 chr12:121454332-121454342 chr12:121454330-121454341 chr12:121454328-121454343 chr12:121454332-121454340
7	TCF12	chr12:121453808-121454737	A549	lung:	n/a	n/a
8	USF2	chr12:121454172-121454501	K562	blood:	n/a	chr12:121454335-121454344 chr12:121454335-121454346 chr12:121454336-121454345 chr12:121454334-121454347 chr12:121454336-121454345
9	CREB1	chr12:121453948-121454661	GM12878	blood:	n/a	chr12:121454329-121454342
10	USF1	chr12:121454205-121454422	HepG2	liver:	n/a	chr12:121454335-121454344 chr12:121454334-121454345 chr12:121454336-121454345 chr12:121454334-121454347 chr12:121454336-121454345
11	YY1	chr12:121453712-121454685	SK-N-SH_RA	brain:	n/a	chr12:121454269-121454281
12	BHLHE40	chr12:121454016-121454506	GM12878	blood:	n/a	chr12:121454335-121454344 chr12:121454336-121454345 chr12:121454334-121454347 chr12:121454336-121454345
13	SIX5	chr12:121454112-121454532	K562	blood:	n/a	chr12:121454366-121454380 chr12:121454369-121454378
14	POLR2A	chr12:121453984-121454455	GM18505	blood:	n/a	n/a
15	GABPA	chr12:121453935-121454470	A549	lung:	n/a	n/a
16	SIN3AK20	chr12:121454078-121454391	PFSK-1	brain:	n/a	n/a
17	TCF12	chr12:121454105-121454546	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:121453966-121454483	PANC-1	pancreas:	n/a	n/a
19	TAF1	chr12:121454006-121454356	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr12:121453997-121454617	GM12878	blood:	n/a	n/a
21	SIN3AK20	chr12:121454039-121454509	A549	lung:	n/a	n/a
22	TBP	chr12:121454046-121454488	HepG2	liver:	n/a	n/a
23	REST	chr12:121453436-121454718	H1-neurons	neurons:	n/a	n/a
24	SIX5	chr12:121453710-121454799	A549	lung:	n/a	chr12:121454366-121454380 chr12:121454369-121454378
25	HEY1	chr12:121453992-121454391	K562	blood:	n/a	chr12:121454330-121454339 chr12:121454332-121454341
26	GTF2F1	chr12:121453953-121454551	Hela-S3	cervix:	n/a	n/a
27	JUND	chr12:121454116-121454540	K562	blood:	n/a	chr12:121454331-121454340
28	MXI1	chr12:121453942-121454637	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:121454041-121454385	GM12891	blood:	n/a	n/a
30	POLR2A	chr12:121454002-121454453	IMR90	lung:	n/a	n/a
31	TAF1	chr12:121454062-121454456	PFSK-1	brain:	n/a	n/a
32	ETS1	chr12:121453924-121454640	K562	blood:	n/a	chr12:121454366-121454379 chr12:121454367-121454380
33	CTCF	chr12:121454042-121454399	GM12878	blood:	n/a	n/a
34	BRCA1	chr12:121454063-121454562	Hela-S3	cervix:	n/a	n/a
35	EP300	chr12:121454096-121454541	SK-N-SH_RA	brain:	n/a	n/a
36	MAZ	chr12:121454032-121454483	Hela-S3	cervix:	n/a	chr12:121454336-121454345
37	POLR2A	chr12:121454060-121454451	A549	lung:	n/a	n/a
38	GTF2F1	chr12:121454178-121454529	K562	blood:	n/a	n/a
39	MYBL2	chr12:121453881-121454572	HepG2	liver:	n/a	n/a
40	YY1	chr12:121453673-121454665	K562	blood:	n/a	chr12:121454269-121454281
41	YY1	chr12:121453620-121454760	A549	lung:	n/a	chr12:121454269-121454281
42	SP1	chr12:121453892-121454649	A549	lung:	n/a	chr12:121454092-121454102
43	YY1	chr12:121453728-121454688	GM12892	blood:	n/a	chr12:121454269-121454281
44	MAX	chr12:121453965-121454460	K562	blood:	n/a	chr12:121454336-121454345
45	USF1	chr12:121454125-121454531	A549	lung:	n/a	chr12:121454335-121454344 chr12:121454334-121454345 chr12:121454336-121454345 chr12:121454334-121454347 chr12:121454336-121454345
46	POLR2A	chr12:121454058-121454394	HepG2	liver:	n/a	n/a
47	TBP	chr12:121454085-121454580	GM12878	blood:	n/a	n/a
48	JUN	chr12:121453564-121454860	K562	blood:	n/a	chr12:121453739-121453750 chr12:121454327-121454340 chr12:121454331-121454340
49	POLR2A	chr12:121453667-121454440	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr12:121453962-121454468	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:121454272-121454322	HRCEpiC	kidney:	n/a
2	chr12:121454269-121454319	GM19239	blood:	n/a
3	chr12:121454272-121454322	U87	brain:	n/a
4	chr12:121454288-121454338	HIPEpiC	eye:	n/a
5	chr12:121454288-121454338	HCT-116	colon:	n/a
6	chr12:121454272-121454322	HNPCEpiC	eye:	n/a
7	chr12:121454272-121454322	HIPEpiC	eye:	n/a
8	chr12:121454269-121454319	H1-hESC	embryonic stem cell:	embryo
9	chr12:121454288-121454338	Hepatocyte	liver:	n/a
10	chr12:121454288-121454338	HRCEpiC	kidney:	n/a
11	chr12:121454272-121454322	PFSK-1	brain:	n/a
12	chr12:121454269-121454319	NHDF-neo	bronchial:	n/a
13	chr12:121454269-121454319	U87	brain:	n/a
14	chr12:121454269-121454319	HIPEpiC	eye:	n/a
15	chr12:121454269-121454319	LNCaP	prostate:	n/a
16	chr12:121454272-121454322	HPAEpiC	pulmonary alveolar:	n/a
17	chr12:121454269-121454319	HUVEC	blood vessel:	n/a
18	chr12:121454272-121454322	NT2-D1	testis:	n/a
19	chr12:121454272-121454322	HEEpiC	esophagus:	n/a
20	chr12:121454269-121454319	HRPEpiC	eye:	n/a
21	chr12:121454272-121454322	NH-A	brain:	n/a
22	chr12:121454288-121454338	GM06990	blood:	n/a
23	chr12:121454272-121454322	HMEC	breast:	n/a
24	chr12:121454272-121454322	IMR90	lung:	fetal
25	chr12:121454269-121454319	HRE	kidney:	n/a
26	chr12:121454288-121454338	NB4	blood:	n/a
27	chr12:121454288-121454338	SK-N-SH_RA	brain:	n/a
28	chr12:121454272-121454322	HAEpiC	amniotic membrane:	n/a
29	chr12:121454288-121454338	AG04449	skin:	fetal
30	chr12:121454269-121454319	SKMC	muscle:	n/a
31	chr12:121454288-121454338	NH-A	brain:	n/a
32	chr12:121454269-121454319	HEK293	kidney:	embryo
33	chr12:121454272-121454322	GM12878	blood:	n/a
34	chr12:121454288-121454338	HCF	heart:	n/a
35	chr12:121454288-121454338	PANC-1	pancreas:	n/a
36	chr12:121454288-121454338	GM19239	blood:	n/a
37	chr12:121454269-121454319	HAEpiC	amniotic membrane:	n/a
38	chr12:121454272-121454322	HepG2	liver:	n/a
39	chr12:121454272-121454322	HCM	heart:	n/a
40	chr12:121454269-121454319	GM12892	blood:	n/a
41	chr12:121454272-121454322	MCF-7	breast:	n/a
42	chr12:121454269-121454319	HMEC	breast:	n/a
43	chr12:121454269-121454319	IMR90	lung:	fetal
44	chr12:121454288-121454338	AoSMC	blood vessel:	n/a
45	chr12:121454269-121454319	ovcar-3	ovarian:	n/a
46	chr12:121454269-121454319	GM12891	blood:	n/a
47	chr12:121454288-121454338	MCF10A-Er-Src	breast:	n/a
48	chr12:121454272-121454322	HL-60	blood:	n/a
49	chr12:121454269-121454319	AG04450	lung:	fetal
50	chr12:121454272-121454322	Hela-S3	cervix:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121445828..121450860-chr12:121451549..121454387,9	K562	blood:
2	chr12:121452592..121454438-chr12:121647839..121649379,2	MCF-7	breast:
3	chr12:121445828..121451054-chr12:121451445..121454709,11	K562	blood:
4	chr12:121442812..121445650-chr12:121451524..121454471,3	K562	blood:
5	chr12:121447431..121451051-chr12:121452490..121455717,3	MCF-7	breast:

Variant related genes	Relation type
C12orf43	TF binding region
C12orf43	CpG island
ENSG00000135124	Chromatin interaction
ENSG00000157895	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10849829	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.86[MKK][hapmap];0.83[ASN][1000 genomes]
rs1169279	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169281	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169299	0.95[ASN][1000 genomes]
rs1169300	0.91[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1169301	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1169302	0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs1169303	0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1169312	0.86[MEX][hapmap]
rs1169313	0.86[MEX][hapmap]
rs1169314	0.87[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1169315	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182933	0.96[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2254971	0.95[ASN][1000 genomes]
rs2257764	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2258043	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2259690	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2259693	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2259777	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2259816	0.86[MEX][hapmap]
rs2259820	0.95[MEX][hapmap];0.97[TSI][hapmap]
rs2259883	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs2260399	0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2260445	0.84[ASN][1000 genomes]
rs2260446	0.84[ASN][1000 genomes]
rs2264750	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2264778	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2464196	0.91[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2701189	0.81[ASN][1000 genomes]
rs2708081	0.87[MKK][hapmap];0.85[YRI][hapmap]
rs3213545	0.83[CEU][hapmap]
rs4278584	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs735396	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1039216	chr12:121421701-121538491	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2258287	CABP1	cis	cerebellum	SCAN
rs2258287	FLJ12448	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121452800-121454400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:121452800-121454400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:121452800-121454400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr12:121452800-121454400	Active TSS	HSMM	muscle
5	chr12:121452800-121454400	Active TSS	NH-A	brain
6	chr12:121453000-121454400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:121453000-121454400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:121453000-121454400	Active TSS	NHLF	lung
9	chr12:121453200-121454400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:121453200-121454400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr12:121453200-121454400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr12:121453200-121454400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:121453200-121454400	Active TSS	Fetal Intestine Large	intestine
14	chr12:121453200-121454400	Active TSS	K562	blood
15	chr12:121453400-121454400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:121453400-121454400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr12:121453400-121454400	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:121453400-121454400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr12:121453400-121454400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:121453400-121454400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:121453400-121454400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:121453400-121454400	Active TSS	Fetal Muscle Leg	muscle
23	chr12:121453400-121454400	Active TSS	HMEC	breast
24	chr12:121453400-121454400	Active TSS	HSMMtube	muscle
25	chr12:121453400-121454600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:121453400-121454600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:121453400-121454600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:121453400-121454600	Active TSS	Colonic Mucosa	Colon
29	chr12:121453400-121454600	Active TSS	A549	lung
30	chr12:121453400-121454600	Active TSS	NHDF-Ad	bronchial
31	chr12:121453600-121454400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:121453600-121454400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:121453600-121454400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:121453600-121454400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr12:121453600-121454400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr12:121453600-121454400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:121453600-121454400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr12:121453600-121454400	Active TSS	Fetal Intestine Small	intestine
39	chr12:121453600-121454400	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr12:121453600-121454400	Active TSS	Fetal Stomach	stomach
41	chr12:121453600-121454400	Active TSS	Left Ventricle	heart
42	chr12:121453600-121454400	Active TSS	Lung	lung
43	chr12:121453600-121454400	Active TSS	Ovary	ovary
44	chr12:121453600-121454400	Active TSS	Placenta Amnion	Placenta Amnion
45	chr12:121453600-121454400	Active TSS	GM12878-XiMat	blood
46	chr12:121453600-121454400	Active TSS	Hela-S3	cervix
47	chr12:121453600-121454600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:121453600-121454600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr12:121453600-121454600	Active TSS	Aorta	Aorta
50	chr12:121453800-121454400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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