Variant report

Variant	rs2732439
Chromosome Location	chr12:48744199-48744200
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	CHD2	chr12:48743920-48745171	GM12878	blood:	n/a	n/a
2	TCF7L2	chr12:48744071-48745162	HCT-116	colon:	n/a	n/a
3	GTF2F1	chr12:48744038-48744340	Hela-S3	cervix:	n/a	n/a
4	TBP	chr12:48744077-48744366	H1-hESC	embryonic stem cell:	n/a	n/a
5	GABPA	chr12:48744071-48744821	A549	lung:	n/a	chr12:48744732-48744741
6	SPI1	chr12:48743851-48744357	GM12891	blood:	n/a	chr12:48743959-48743968
7	SIN3AK20	chr12:48744111-48744765	SK-N-SH	brain:	n/a	n/a
8	CEBPB	chr12:48744031-48745673	Hela-S3	cervix:	n/a	chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745055-48745066
9	MAX	chr12:48743927-48745480	ECC-1	luminal epithelium:	n/a	chr12:48744116-48744126
10	TBP	chr12:48744199-48745295	K562	blood:	n/a	n/a
11	POLR2A	chr12:48744139-48745058	MCF-7	breast:	n/a	n/a
12	STAT5A	chr12:48744014-48744484	GM12878	blood:	n/a	n/a
13	TAF1	chr12:48743935-48745219	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr12:48744147-48745291	IMR90	lung:	n/a	n/a
15	MAFK	chr12:48744005-48744468	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr12:48744178-48745233	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:48744019-48745190	ECC-1	luminal epithelium:	n/a	n/a
18	RCOR1	chr12:48744022-48745333	Hela-S3	cervix:	n/a	n/a
19	TAF1	chr12:48743979-48744446	H1-hESC	embryonic stem cell:	n/a	n/a
20	TEAD4	chr12:48744022-48744477	K562	blood:	n/a	n/a
21	ESR1	chr12:48744099-48744347	ECC-1	luminal epithelium:	n/a	chr12:48744186-48744203
22	TEAD4	chr12:48744006-48745360	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr12:48744065-48745387	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr12:48744070-48745243	HepG2	liver:	n/a	n/a
25	POLR2A	chr12:48744064-48744430	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr12:48744079-48744403	Hela-S3	cervix:	n/a	n/a
27	MAX	chr12:48743956-48745378	A549	lung:	n/a	chr12:48744116-48744126
28	ELF1	chr12:48744141-48744940	GM12878	blood:	n/a	chr12:48744628-48744640 chr12:48744739-48744748 chr12:48744446-48744457
29	ZKSCAN1	chr12:48744063-48745288	Hela-S3	cervix:	n/a	n/a
30	MAX	chr12:48744108-48744503	HepG2	liver:	n/a	chr12:48744116-48744126
31	POLR2A	chr12:48744023-48745087	GM18526	blood:	n/a	n/a
32	POLR2A	chr12:48744154-48745306	SK-N-MC	brain:	n/a	n/a
33	BRCA1	chr12:48743894-48745495	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr12:48744111-48745235	HCT-116	colon:	n/a	n/a
35	POLR2A	chr12:48744059-48745168	GM12892	blood:	n/a	n/a
36	GABPA	chr12:48744010-48745215	MCF-7	breast:	n/a	chr12:48744933-48744942 chr12:48744884-48744893 chr12:48744732-48744741
37	POLR2A	chr12:48743780-48745367	Hela-S3	cervix:	n/a	n/a
38	EP300	chr12:48744098-48745343	ECC-1	luminal epithelium:	n/a	chr12:48744745-48744761 chr12:48744492-48744508 chr12:48744884-48744893 chr12:48744889-48744905 chr12:48744933-48744942
39	ELK1	chr12:48744184-48745319	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:48744032-48745338	K562	blood:	n/a	n/a
41	SPI1	chr12:48744123-48744331	K562	blood:	n/a	n/a
42	GABPA	chr12:48744063-48744491	Hela-S3	cervix:	n/a	n/a
43	HCFC1	chr12:48744179-48745241	K562	blood:	n/a	n/a
44	TCF12	chr12:48744061-48744378	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr12:48744105-48745288	H1-neurons	neurons:	n/a	n/a
46	NR2F2	chr12:48744007-48744603	MCF-7	breast:	n/a	n/a
47	MAX	chr12:48743924-48745347	MCF-7	breast:	n/a	chr12:48744116-48744126
48	ESR1	chr12:48743989-48744436	ECC-1	luminal epithelium:	n/a	chr12:48744186-48744203
49	POLR2A	chr12:48744086-48745344	Hela-S3	cervix:	n/a	n/a
50	SMARCB1	chr12:48743968-48745386	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48743746..48745739-chr15:100880509..100882154,2	MCF-7	breast:
2	chr12:48743811..48746136-chr12:49207748..49210431,2	MCF-7	breast:
3	chr12:48738698..48740838-chr12:48743123..48744667,2	K562	blood:
4	chr12:48744164..48745071-chr20:32581340..32582207,2	Hela-S3	cervix:
5	chr12:48721748..48724371-chr12:48742736..48744281,2	K562	blood:
6	chr12:48740296..48746434-chr12:48748194..48754526,9	MCF-7	breast:
7	chr12:48737402..48739098-chr12:48743829..48745442,2	MCF-7	breast:
8	chr12:48744030..48746480-chr12:48749780..48752086,4	K562	blood:
9	chr12:48741301..48746348-chr12:48747901..48753728,9	MCF-7	breast:
10	chr12:48737714..48740514-chr12:48742056..48744740,4	K562	blood:
11	chr12:48743415..48745587-chr12:48758145..48761066,2	MCF-7	breast:
12	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:
13	chr12:48590039..48593666-chr12:48742360..48744824,3	K562	blood:
14	chr10:74385755..74386435-chr12:48744037..48744930,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-H1FNT-1	chr12:48744141-48744573	NONHSAT027994

Variant related genes	Relation type
ENSG00000257735	TF binding region
ENSG00000258273	Chromatin interaction
ENSG00000228265	Chromatin interaction
ENSG00000269514	Chromatin interaction
ENSG00000107745	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000187166	Chromatin interaction
ENSG00000167528	Chromatin interaction
ENSG00000257763	Chromatin interaction
ENSG00000140470	Chromatin interaction
ENSG00000269282	Chromatin interaction
ENSG00000125970	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10431526	0.83[ASN][1000 genomes]
rs10467101	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs10875750	0.87[JPT][hapmap]
rs10875767	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs10875770	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10875772	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10875792	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875793	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875799	0.95[ASN][1000 genomes]
rs11168433	0.87[JPT][hapmap]
rs11168450	0.87[JPT][hapmap]
rs11168459	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11168508	0.81[ASN][1000 genomes]
rs11168510	0.82[ASN][1000 genomes]
rs11168514	0.83[ASN][1000 genomes]
rs11168516	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11168520	0.92[ASN][1000 genomes]
rs11168536	0.95[ASN][1000 genomes]
rs12227601	0.81[ASN][1000 genomes]
rs12305511	0.87[JPT][hapmap]
rs12312134	0.81[JPT][hapmap]
rs12313745	0.91[ASN][1000 genomes]
rs12322347	0.91[ASN][1000 genomes]
rs12322348	0.91[ASN][1000 genomes]
rs1471997	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17122812	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2012773	0.87[JPT][hapmap]
rs2054903	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2054904	0.93[ASN][1000 genomes]
rs2279464	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2450992	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2634675	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732465	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3185921	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3751273	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs4760622	0.87[JPT][hapmap]
rs4760625	0.81[ASN][1000 genomes]
rs4760687	0.87[JPT][hapmap]
rs4760695	0.87[JPT][hapmap]
rs4760696	0.87[JPT][hapmap]
rs4760697	0.87[JPT][hapmap]
rs6580659	0.85[JPT][hapmap]
rs7135779	0.85[JPT][hapmap]
rs7297298	0.81[ASN][1000 genomes]
rs7486424	0.87[JPT][hapmap]
rs9634261	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv1045159	chr12:48730024-48748940	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2732439	H1FNT	cis	Muscle Skeletal	GTEx
rs2732439	ZNF641	cis	Thyroid	GTEx
rs2732439	ZNF641	cis	Whole Blood	GTEx
rs2732439	ZNF641	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48743000-48744200	Flanking Active TSS	Osteobl	bone
2	chr12:48743000-48744400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:48743000-48745600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr12:48743200-48744200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:48743200-48744200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr12:48743200-48744200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr12:48743200-48744200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr12:48743200-48744200	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr12:48743200-48744200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr12:48743200-48744200	Flanking Active TSS	Thymus	Thymus
11	chr12:48743200-48744200	Flanking Active TSS	Hela-S3	cervix
12	chr12:48743200-48744400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr12:48743200-48744400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr12:48743200-48744400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:48743200-48744400	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr12:48743200-48745400	Active TSS	Ovary	ovary
17	chr12:48743200-48745600	Active TSS	Right Atrium	heart
18	chr12:48743400-48744200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:48743400-48744200	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr12:48743400-48744200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr12:48743400-48744200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr12:48743400-48744200	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr12:48743400-48744200	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr12:48743400-48744200	Flanking Active TSS	Fetal Brain Female	brain
25	chr12:48743400-48744200	Flanking Active TSS	Fetal Intestine Large	intestine
26	chr12:48743400-48744200	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr12:48743400-48744200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr12:48743400-48744200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr12:48743400-48744400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr12:48743400-48744400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr12:48743400-48744400	Flanking Active TSS	Dnd41	blood
32	chr12:48743400-48745200	Active TSS	GM12878-XiMat	blood
33	chr12:48743600-48744200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:48743600-48744200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr12:48743600-48744200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:48743600-48744200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:48743600-48744200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:48743600-48744200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:48743600-48744200	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr12:48743600-48744200	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr12:48743600-48744200	Flanking Active TSS	Fetal Brain Male	brain
42	chr12:48743600-48744200	Flanking Active TSS	Fetal Lung	lung
43	chr12:48743600-48744200	Flanking Active TSS	Psoas Muscle	Psoas
44	chr12:48743600-48744200	Flanking Active TSS	A549	lung
45	chr12:48743600-48744200	Flanking Active TSS	NHLF	lung
46	chr12:48743600-48744400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:48743600-48744400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:48743600-48744400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:48743600-48744400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr12:48743600-48744400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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