Variant report

Variant	rs1669297
Chromosome Location	chr12:57940071-57940072
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	chr12:57939787-57940527	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr12:57940041-57940142	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:57939907-57941301	U87	brain:	n/a	n/a
4	JUND	chr12:57939823-57940307	K562	blood:	n/a	chr12:57940013-57940024 chr12:57940233-57940241 chr12:57940232-57940242
5	STAT3	chr12:57939908-57940348	MCF10A-Er-Src	breast:	n/a	n/a
6	MAZ	chr12:57939889-57941309	K562	blood:	n/a	n/a
7	HCFC1	chr12:57939899-57940341	K562	blood:	n/a	n/a
8	ZBTB33	chr12:57940015-57941446	A549	lung:	n/a	chr12:57940975-57940984 chr12:57941015-57941025 chr12:57941009-57941024 chr12:57940970-57940985
9	HEY1	chr12:57939856-57940259	K562	blood:	n/a	n/a
10	FOS	chr12:57939901-57940333	MCF10A-Er-Src	breast:	n/a	chr12:57940013-57940024 chr12:57940233-57940241 chr12:57940232-57940242
11	POLR2A	chr12:57939877-57941250	K562	blood:	n/a	n/a
12	ATF3	chr12:57939741-57940134	K562	blood:	n/a	n/a
13	FOXA1	chr12:57939801-57940179	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:57939818-57941257	HUVEC	blood vessel:	n/a	n/a
15	TCF12	chr12:57939800-57941009	A549	lung:	n/a	chr12:57940018-57940027 chr12:57940006-57940016
16	POLR2A	chr12:57939980-57940371	HepG2	liver:	n/a	n/a
17	BHLHE40	chr12:57939941-57940536	K562	blood:	n/a	n/a
18	POLR2A	chr12:57939784-57940400	HepG2	liver:	n/a	n/a
19	FOXA2	chr12:57939859-57940153	HepG2	liver:	n/a	n/a
20	CTCF	chr12:57940040-57940190	A549	lung:	n/a	n/a
21	POLR2A	chr12:57939600-57941148	H1-hESC	embryonic stem cell:	n/a	n/a
22	MTA3	chr12:57939677-57941261	GM12878	blood:	n/a	n/a
23	TEAD4	chr12:57939508-57940335	K562	blood:	n/a	n/a
24	POLR2A	chr12:57940067-57940136	ProgFib	skin:	n/a	n/a
25	MAX	chr12:57939885-57940242	K562	blood:	n/a	n/a
26	POLR2A	chr12:57939775-57941262	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr12:57939749-57941238	GM12892	blood:	n/a	n/a
28	MAX	chr12:57939731-57940689	K562	blood:	n/a	n/a
29	USF2	chr12:57939928-57940513	Hela-S3	cervix:	n/a	n/a
30	ZMIZ1	chr12:57939984-57940244	K562	blood:	n/a	n/a
31	POLR2A	chr12:57939807-57941316	K562	blood:	n/a	n/a
32	MAX	chr12:57939903-57940123	HepG2	liver:	n/a	n/a
33	MYC	chr12:57939922-57940392	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr12:57939925-57941261	U87	brain:	n/a	n/a
35	HEY1	chr12:57939766-57941144	K562	blood:	n/a	n/a
36	MXI1	chr12:57939980-57940163	H1-hESC	embryonic stem cell:	n/a	chr12:57940006-57940015
37	POLR2A	chr12:57939884-57941409	PBDE	blood:	n/a	n/a
38	POLR2A	chr12:57939810-57940634	GM12892	blood:	n/a	n/a
39	CHD2	chr12:57939878-57941333	HepG2	liver:	n/a	chr12:57940975-57940984
40	HEY1	chr12:57939826-57940210	HepG2	liver:	n/a	n/a
41	NR2F2	chr12:57939665-57941401	K562	blood:	n/a	n/a
42	USF2	chr12:57940040-57940102	K562	blood:	n/a	n/a
43	YY1	chr12:57939795-57940181	K562	blood:	n/a	n/a
44	STAT3	chr12:57939868-57940324	MCF10A-Er-Src	breast:	n/a	n/a
45	POU2F2	chr12:57939670-57940131	GM12891	blood:	n/a	chr12:57939948-57939956
46	POLR2A	chr12:57939549-57941260	K562	blood:	n/a	n/a
47	POLR2A	chr12:57939992-57941220	HUVEC	blood vessel:	n/a	n/a
48	SMC3	chr12:57939977-57940551	HepG2	liver:	n/a	n/a
49	STAT3	chr12:57939907-57940349	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr12:57939895-57941549	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57881658..57883601-chr12:57939659..57941613,2	MCF-7	breast:
2	chr12:57938852..57941348-chr12:58005104..58006975,2	K562	blood:
3	chr12:57938950..57942640-chr12:57942750..57946701,7	K562	blood:
4	chr12:57939429..57943777-chr12:57984797..57987088,3	K562	blood:
5	chr12:57939451..57941325-chr12:58024374..58027583,3	K562	blood:
6	chr12:57939583..57941703-chr12:58002111..58004794,2	K562	blood:
7	chr12:57939918..57942387-chr12:58138816..58141058,2	K562	blood:
8	chr12:57935626..57940631-chr12:58026197..58030320,5	K562	blood:
9	chr12:57881482..57885096-chr12:57938469..57941069,3	K562	blood:
10	chr12:57929188..57932764-chr12:57939481..57941098,3	MCF-7	breast:

Variant related genes	Relation type
KIF5A	TF binding region
DCTN2	TF binding region
ENSG00000166908	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000155980	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000135454	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1148552	0.84[AFR][1000 genomes]
rs1148553	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1148554	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148555	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148557	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1284465	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1284605	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1299737	0.84[EUR][1000 genomes]
rs1629410	0.88[EUR][1000 genomes]
rs1669294	0.84[EUR][1000 genomes]
rs1669296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678537	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1679368	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1709871	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1709874	0.83[EUR][1000 genomes]
rs2127318	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2620677	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2620679	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2928382	0.83[EUR][1000 genomes]
rs2943696	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782129	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3847699	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs474544	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760273	0.80[EUR][1000 genomes]
rs496245	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs697221	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703835	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs703836	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs703837	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs703838	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703839	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7299631	0.99[EUR][1000 genomes]
rs747340	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs775236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775241	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs775323	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs775324	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs776038	0.84[EUR][1000 genomes]
rs776039	0.84[EUR][1000 genomes]
rs7964074	0.97[EUR][1000 genomes]
rs796546	0.84[EUR][1000 genomes]
rs9737891	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
2	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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	126 gene(s)	inside rSNPs	diseases
9	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
10	nsv1053930	chr12:57921188-57969659	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57937200-57940200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr12:57938600-57940800	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr12:57939000-57940200	Enhancers	Primary T cells from cord blood	blood
4	chr12:57939200-57940200	Transcr. at gene 5' and 3'	K562	blood
5	chr12:57939200-57940200	Flanking Active TSS	NHDF-Ad	bronchial
6	chr12:57939200-57940400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:57939400-57940200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:57939400-57940200	Flanking Active TSS	Colon Smooth Muscle	Colon
9	chr12:57939400-57940200	Flanking Active TSS	GM12878-XiMat	blood
10	chr12:57939400-57940200	Flanking Active TSS	HepG2	liver
11	chr12:57939400-57940400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:57939400-57940400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr12:57939400-57940400	Flanking Active TSS	Fetal Brain Female	brain
14	chr12:57939600-57940200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:57939600-57940200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:57939600-57940200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr12:57939600-57940200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr12:57939600-57940200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:57939600-57940200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:57939600-57940200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:57939600-57940200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:57939600-57940200	Enhancers	Spleen	Spleen
23	chr12:57939600-57940200	Flanking Active TSS	HMEC	breast
24	chr12:57939600-57940400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:57939600-57940400	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr12:57939600-57940400	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr12:57939600-57940400	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr12:57939600-57940400	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr12:57939600-57940400	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr12:57939600-57940400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr12:57939600-57940400	Flanking Active TSS	Colonic Mucosa	Colon
32	chr12:57939600-57940400	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr12:57939600-57940400	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr12:57939600-57940400	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr12:57939600-57940400	Flanking Active TSS	Pancreas	Pancrea
36	chr12:57939600-57940400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr12:57939600-57940400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr12:57939600-57940400	Flanking Active TSS	Rectal Smooth Muscle	rectum
39	chr12:57939600-57940400	Flanking Active TSS	Right Ventricle	heart
40	chr12:57939600-57940400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr12:57939600-57940400	Flanking Active TSS	HSMMtube	muscle
42	chr12:57939600-57940400	Flanking Active TSS	NH-A	brain
43	chr12:57939600-57940400	Transcr. at gene 5' and 3'	NHLF	lung
44	chr12:57939600-57940400	Flanking Active TSS	Osteobl	bone
45	chr12:57939600-57940600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:57939600-57940600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr12:57939600-57940600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr12:57939600-57941400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr12:57939800-57940200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:57939800-57940200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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