Variant report

Variant	rs7968403
Chromosome Location	chr12:65012824-65012825
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	RUNX3	chr12:65012747-65013400	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:65012770-65013352	GM12878	blood:	n/a	n/a
3	TEAD4	chr12:65012733-65013349	K562	blood:	n/a	n/a
4	CEBPB	chr12:65012788-65013423	GM12878	blood:	n/a	chr12:65013308-65013325
5	IRF1	chr12:65012818-65013394	K562	blood:	n/a	chr12:65013084-65013091
6	POLR2A	chr12:65012815-65013254	GM12891	blood:	n/a	n/a
7	MTA3	chr12:65012751-65013365	GM12878	blood:	n/a	n/a
8	TEAD4	chr12:65012744-65013452	K562	blood:	n/a	n/a
9	ARID3A	chr12:65012823-65013421	K562	blood:	n/a	n/a
10	NR2F2	chr12:65012802-65013323	K562	blood:	n/a	n/a
11	POU2F2	chr12:65012757-65013081	GM12891	blood:	n/a	n/a
12	EP300	chr12:65012819-65013402	K562	blood:	n/a	n/a
13	CEBPB	chr12:65012764-65013390	K562	blood:	n/a	chr12:65013308-65013325
14	IRF1	chr12:65012738-65013348	K562	blood:	n/a	chr12:65013084-65013091
15	MAX	chr12:65012750-65013094	K562	blood:	n/a	n/a
16	PML	chr12:65012736-65013610	GM12878	blood:	n/a	n/a
17	BCLAF1	chr12:65012782-65013345	GM12878	blood:	n/a	n/a
18	CEBPD	chr12:65012806-65013404	K562	blood:	n/a	chr12:65013078-65013089
19	CEBPB	chr12:65012610-65014099	K562	blood:	n/a	chr12:65013308-65013325
20	ATF2	chr12:65012800-65013454	GM12878	blood:	n/a	n/a
21	EBF1	chr12:65012793-65013220	GM12878	blood:	n/a	n/a
22	NFIC	chr12:65012630-65013380	GM12878	blood:	n/a	n/a
23	NR2F2	chr12:65012786-65013393	K562	blood:	n/a	n/a
24	STAT5A	chr12:65012780-65013315	K562	blood:	n/a	n/a
25	SPI1	chr12:65012824-65013333	HL-60	blood:	n/a	chr12:65013102-65013115 chr12:65013002-65013015 chr12:65013101-65013114 chr12:65013004-65013013
26	TAL1	chr12:65012786-65013324	K562	blood:	n/a	n/a
27	CEBPD	chr12:65012789-65013352	K562	blood:	n/a	chr12:65013078-65013089
28	FOXM1	chr12:65012737-65013438	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:65012784-65013392	GM12892	blood:	n/a	n/a
30	POLR2A	chr12:65012792-65013261	K562	blood:	n/a	n/a
31	STAT5A	chr12:65012736-65013313	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:65012819-65013398	GM12891	blood:	n/a	n/a
33	FOXM1	chr12:65012814-65013474	GM12878	blood:	n/a	n/a
34	ZNF143	chr12:65012819-65013274	GM12878	blood:	n/a	n/a
35	NFIC	chr12:65012732-65013291	GM12878	blood:	n/a	n/a
36	NFATC1	chr12:65012721-65013362	GM12878	blood:	n/a	n/a
37	REST	chr12:65012812-65013272	K562	blood:	n/a	n/a
38	MXI1	chr12:65012796-65013183	K562	blood:	n/a	n/a
39	NFATC1	chr12:65012814-65013296	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:65012755-65013534	GM12878	blood:	n/a	n/a
41	ATF2	chr12:65012809-65013472	GM12878	blood:	n/a	n/a
42	IRF4	chr12:65012808-65013267	GM12878	blood:	n/a	n/a
43	GATA2	chr12:65012780-65013319	K562	blood:	n/a	chr12:65013283-65013290 chr12:65013106-65013117
44	BCL3	chr12:65012816-65013390	A549	lung:	n/a	n/a
45	PML	chr12:65012820-65013377	K562	blood:	n/a	n/a
46	BCLAF1	chr12:65012818-65013490	GM12878	blood:	n/a	n/a
47	MAX	chr12:65012800-65013302	K562	blood:	n/a	n/a
48	POLR2A	chr12:65012824-65013372	GM12892	blood:	n/a	n/a
49	CUX1	chr12:65012824-65013278	K562	blood:	n/a	n/a
50	MTA3	chr12:65012765-65013485	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:65011741..65013304-chr12:65014753..65016966,2	MCF-7	breast:
2	chr12:65011047..65013425-chr12:65022632..65024706,2	MCF-7	breast:
3	chr12:65011462..65014885-chr12:65017332..65020916,6	MCF-7	breast:
4	chr12:65010556..65012937-chr12:65017376..65021348,4	K562	blood:
5	chr12:64960849..64962963-chr12:65011488..65013311,2	K562	blood:
6	chr12:65011593..65014021-chr12:65067404..65069519,2	K562	blood:

Variant related genes	Relation type
MIR548C	TF binding region
ENSG00000207546	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10784417	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784418	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175483	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11175484	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1147105	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1147107	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1244869	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1244873	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1244878	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1245168	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1245169	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1245179	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1245180	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1245181	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1245183	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1245184	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1245185	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1245186	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1245187	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1264485	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1268914	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1270437	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1270836	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1270837	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1272547	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1383117	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1690259	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1690272	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1690273	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1716490	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1716496	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1716506	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1716517	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795613	0.93[ASN][1000 genomes]
rs1795618	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1795621	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1795622	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1795624	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1795625	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1797678	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1797679	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1797684	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1797688	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1797689	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2464347	0.93[ASN][1000 genomes]
rs2620730	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682714	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682716	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2682719	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682728	0.81[EUR][1000 genomes]
rs2701849	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2701850	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7313651	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7313765	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7971636	0.93[ASN][1000 genomes]
rs7975455	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription 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	27 gene(s)	inside rSNPs	diseases
2	nsv1048199	chr12:64951666-65021700	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv541512	chr12:64951666-65021700	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS 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	15 gene(s)	inside rSNPs	diseases
9	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 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	chr12:65005800-65015200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:65005800-65017800	Weak transcription	Gastric	stomach
3	chr12:65006200-65013000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:65006200-65017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:65006200-65017600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:65006200-65018800	Weak transcription	Fetal Thymus	thymus
7	chr12:65006200-65019000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:65006200-65019000	Weak transcription	NHEK	skin
9	chr12:65006200-65019400	Weak transcription	Psoas Muscle	Psoas
10	chr12:65006400-65017000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:65006600-65017400	Weak transcription	Small Intestine	intestine
12	chr12:65006600-65018200	Weak transcription	Fetal Intestine Large	intestine
13	chr12:65006800-65013000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:65006800-65031800	Weak transcription	Dnd41	blood
15	chr12:65007000-65014800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr12:65007000-65018800	Weak transcription	HMEC	breast
17	chr12:65007000-65019200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:65007200-65013000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr12:65007200-65015000	Weak transcription	HepG2	liver
20	chr12:65007200-65017600	Weak transcription	Stomach Mucosa	stomach
21	chr12:65007800-65017600	Weak transcription	Lung	lung
22	chr12:65008600-65019000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:65009000-65013200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:65009200-65019200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:65009800-65013200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr12:65009800-65019200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:65009800-65019400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:65010000-65023200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:65010200-65019400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:65010400-65017000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:65010400-65017000	Weak transcription	NH-A	brain
32	chr12:65010400-65018200	Weak transcription	Colonic Mucosa	Colon
33	chr12:65010400-65019000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:65010600-65013000	Weak transcription	Brain Germinal Matrix	brain
35	chr12:65010600-65013000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr12:65010600-65013000	Weak transcription	Fetal Heart	heart
37	chr12:65010600-65013200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr12:65010600-65013200	Weak transcription	Brain Angular Gyrus	brain
39	chr12:65010600-65017800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr12:65010600-65018800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:65010600-65018800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:65010600-65018800	Weak transcription	Fetal Lung	lung
43	chr12:65010600-65019000	Weak transcription	Fetal Stomach	stomach
44	chr12:65010800-65013800	Enhancers	HUVEC	blood vessel
45	chr12:65010800-65018600	Weak transcription	Fetal Muscle Leg	muscle
46	chr12:65010800-65022200	Weak transcription	Spleen	Spleen
47	chr12:65011000-65018400	Weak transcription	Brain Substantia Nigra	brain
48	chr12:65011200-65013000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:65011200-65018800	Enhancers	Primary B cells from peripheral blood	blood
50	chr12:65011400-65013400	Enhancers	Primary T cells fromperipheralblood	blood

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