Variant report

Variant	rs12299952
Chromosome Location	chr12:57634068-57634069
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	SMC3	chr12:57632187-57634208	SK-N-SH	brain:	n/a	chr12:57632796-57632804 chr12:57633003-57633013 chr12:57633003-57633017 chr12:57634075-57634085 chr12:57632259-57632269
2	POLR2A	chr12:57633629-57634659	GM15510	blood:	n/a	n/a
3	ZBTB7A	chr12:57633994-57634153	K562	blood:	n/a	n/a
4	E2F6	chr12:57633945-57634108	K562	blood:	n/a	n/a
5	MAX	chr12:57633683-57634631	SK-N-SH	brain:	n/a	chr12:57634557-57634566 chr12:57633960-57633969 chr12:57634323-57634333
6	POLR2A	chr12:57632726-57635649	Raji	blood:	n/a	n/a
7	POLR2A	chr12:57632728-57635007	H1-neurons	neurons:	n/a	n/a
8	GATA3	chr12:57633798-57634115	SH-SY5Y	brain:	n/a	n/a
9	RCOR1	chr12:57633733-57634523	GM12878	blood:	n/a	n/a
10	MAX	chr12:57633475-57634824	ECC-1	luminal epithelium:	n/a	chr12:57634557-57634566 chr12:57633960-57633969 chr12:57634323-57634333
11	TAF1	chr12:57633496-57634505	H1-hESC	embryonic stem cell:	n/a	n/a
12	EGR1	chr12:57633997-57634708	K562	blood:	n/a	chr12:57634429-57634442 chr12:57634428-57634442 chr12:57634430-57634441 chr12:57634430-57634440 chr12:57634323-57634333 chr12:57634190-57634203 chr12:57634424-57634446 chr12:57634320-57634333 chr12:57634195-57634210 chr12:57634426-57634440 chr12:57634199-57634208 chr12:57634429-57634442 chr12:57634195-57634205 chr12:57634124-57634137 chr12:57634430-57634440 chr12:57634430-57634441
13	POLR2A	chr12:57632824-57634840	IMR90	lung:	n/a	n/a
14	MAX	chr12:57633602-57634667	H1-hESC	embryonic stem cell:	n/a	chr12:57634557-57634566 chr12:57633960-57633969 chr12:57634323-57634333
15	BHLHE40	chr12:57633889-57634594	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:57633725-57634627	GM19193	blood:	n/a	n/a
17	POLR2A	chr12:57633980-57634487	K562	blood:	n/a	n/a
18	MYC	chr12:57633686-57634647	K562	blood:	n/a	chr12:57634557-57634566 chr12:57633960-57633969 chr12:57634323-57634333
19	SIN3AK20	chr12:57634019-57634569	PFSK-1	brain:	n/a	n/a
20	EGR1	chr12:57634023-57635018	MCF-7	breast:	n/a	chr12:57634429-57634442 chr12:57634790-57634803 chr12:57634428-57634442 chr12:57634430-57634441 chr12:57634430-57634440 chr12:57634323-57634333 chr12:57634190-57634203 chr12:57634424-57634446 chr12:57634320-57634333 chr12:57634195-57634210 chr12:57634426-57634440 chr12:57634199-57634208 chr12:57634429-57634442 chr12:57634195-57634205 chr12:57634124-57634137 chr12:57634430-57634440 chr12:57634795-57634810 chr12:57634430-57634441
21	EGR1	chr12:57634044-57634865	ECC-1	luminal epithelium:	n/a	chr12:57634429-57634442 chr12:57634790-57634803 chr12:57634428-57634442 chr12:57634430-57634441 chr12:57634430-57634440 chr12:57634323-57634333 chr12:57634190-57634203 chr12:57634424-57634446 chr12:57634320-57634333 chr12:57634195-57634210 chr12:57634426-57634440 chr12:57634199-57634208 chr12:57634429-57634442 chr12:57634195-57634205 chr12:57634124-57634137 chr12:57634430-57634440 chr12:57634795-57634810 chr12:57634430-57634441
22	RCOR1	chr12:57634057-57634413	K562	blood:	n/a	n/a
23	SIN3A	chr12:57632041-57635117	H1-hESC	embryonic stem cell:	n/a	chr12:57633985-57633994 chr12:57635049-57635060 chr12:57634171-57634184 chr12:57632501-57632514 chr12:57632476-57632490
24	MAX	chr12:57633506-57634776	ECC-1	luminal epithelium:	n/a	chr12:57634557-57634566 chr12:57633960-57633969 chr12:57634323-57634333
25	MAZ	chr12:57632616-57634738	IMR90	lung:	n/a	chr12:57634557-57634566 chr12:57633323-57633333 chr12:57633960-57633969 chr12:57634323-57634333
26	POLR2A	chr12:57632637-57634824	ECC-1	luminal epithelium:	n/a	n/a
27	JUN	chr12:57633684-57634764	K562	blood:	n/a	chr12:57634158-57634169 chr12:57633963-57633974
28	POLR2A	chr12:57628648-57635024	U87	brain:	n/a	n/a
29	POLR2A	chr12:57631731-57634643	H1-hESC	embryonic stem cell:	n/a	n/a
30	HMGN3	chr12:57633723-57634556	K562	blood:	n/a	n/a
31	POLR2A	chr12:57633565-57634440	SK-N-SH	brain:	n/a	n/a
32	SIN3AK20	chr12:57633923-57635212	MCF-7	breast:	n/a	n/a
33	TAF1	chr12:57633631-57634158	H1-hESC	embryonic stem cell:	n/a	n/a
34	TCF12	chr12:57632552-57634862	A549	lung:	n/a	chr12:57634682-57634689
35	MTA3	chr12:57633900-57635003	GM12878	blood:	n/a	n/a
36	MXI1	chr12:57632428-57635914	IMR90	lung:	n/a	n/a
37	TCF12	chr12:57633588-57634746	ECC-1	luminal epithelium:	n/a	chr12:57634682-57634689
38	CEBPB	chr12:57633747-57634528	IMR90	lung:	n/a	chr12:57633957-57633968
39	MAX	chr12:57633758-57635202	MCF-7	breast:	n/a	chr12:57634557-57634566 chr12:57633960-57633969 chr12:57634323-57634333
40	TCF7L2	chr12:57633967-57634264	PANC-1	pancreas:	n/a	n/a
41	CCNT2	chr12:57633712-57634794	K562	blood:	n/a	chr12:57634195-57634204
42	POLR2A	chr12:57633761-57634607	HCT-116	colon:	n/a	n/a
43	RCOR1	chr12:57633583-57634622	K562	blood:	n/a	n/a
44	MXI1	chr12:57632140-57636615	SK-N-SH	brain:	n/a	n/a
45	CEBPB	chr12:57633793-57634149	H1-hESC	embryonic stem cell:	n/a	chr12:57633957-57633968
46	CEBPB	chr12:57633721-57634693	MCF-7	breast:	n/a	chr12:57633957-57633968
47	JUND	chr12:57633684-57634163	H1-hESC	embryonic stem cell:	n/a	chr12:57633963-57633974
48	POU2F2	chr12:57633888-57634543	GM12891	blood:	n/a	chr12:57634040-57634049
49	POLR2A	chr12:57634055-57634212	A549	lung:	n/a	n/a
50	POLR2A	chr12:57633651-57634588	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57593061..57596040-chr12:57632973..57635946,3	K562	blood:
2	chr12:57633078..57634752-chr12:120728472..120731115,2	MCF-7	breast:
3	chr12:57521132..57523355-chr12:57632415..57635225,2	K562	blood:
4	chr12:57470699..57473429-chr12:57632698..57634398,2	K562	blood:
5	chr12:57503621..57505851-chr12:57632604..57634252,2	K562	blood:
6	chr12:57607529..57608286-chr12:57633745..57634415,2	K562	blood:
7	chr12:57503657..57505571-chr12:57633144..57635959,2	MCF-7	breast:
8	chr12:57480983..57482785-chr12:57632778..57634308,2	MCF-7	breast:
9	chr12:57480809..57483587-chr12:57632653..57634383,3	K562	blood:
10	chr12:57633619..57639143-chr12:57853203..57857806,7	K562	blood:
11	chr12:57632290..57634209-chr12:57884185..57886954,2	K562	blood:
12	chr12:57578498..57581339-chr12:57631776..57634298,3	K562	blood:
13	chr12:57632502..57635395-chr12:58164755..58167639,2	MCF-7	breast:
14	chr12:57633994..57636075-chr12:57915508..57917447,2	MCF-7	breast:
15	chr12:57478737..57483929-chr12:57633097..57638164,8	MCF-7	breast:
16	chr12:57606321..57611608-chr12:57631519..57634473,101	MCF-7	breast:
17	chr12:57631992..57634465-chr12:57823109..57824873,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAC3-1	chr12:57633966-57634278	NONHSAT028897
2	lnc-STAC3-1	chr12:57633329-57634278	NONHSAT028900

Variant related genes	Relation type
NDUFA4L2	TF binding region
ENSG00000166886	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000182379	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10083191	0.84[AFR][1000 genomes]
rs11172151	0.84[AFR][1000 genomes]
rs11172167	0.92[AFR][1000 genomes]
rs12312567	1.00[AFR][1000 genomes]
rs12312780	0.88[AFR][1000 genomes]
rs12315459	0.92[AFR][1000 genomes]
rs12317897	1.00[AFR][1000 genomes]
rs12319006	0.92[AFR][1000 genomes]
rs12320772	0.84[AFR][1000 genomes]
rs35827450	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers 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	181 gene(s)	inside rSNPs	diseases
2	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57628600-57636200	Weak transcription	Hela-S3	cervix
2	chr12:57629000-57634400	Bivalent Enhancer	Stomach Mucosa	stomach
3	chr12:57631400-57634400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:57631600-57634600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:57631600-57635000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:57631600-57635600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:57631800-57634200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr12:57631800-57634200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr12:57631800-57634200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:57631800-57634400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:57631800-57634800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr12:57631800-57634800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:57631800-57634800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
14	chr12:57631800-57635000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:57631800-57635000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
16	chr12:57631800-57635200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr12:57632000-57634400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr12:57632000-57634400	Active TSS	Brain Angular Gyrus	brain
19	chr12:57632000-57634800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
20	chr12:57632000-57635000	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr12:57632000-57635000	Flanking Active TSS	Right Ventricle	heart
22	chr12:57632000-57635000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
23	chr12:57632000-57635200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
24	chr12:57632200-57634200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:57632200-57634200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr12:57632200-57635200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:57632400-57634200	Enhancers	Lung	lung
28	chr12:57632400-57634400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:57632400-57634400	Active TSS	NHDF-Ad	bronchial
30	chr12:57632400-57634400	Flanking Active TSS	Osteobl	bone
31	chr12:57632400-57634600	Flanking Active TSS	K562	blood
32	chr12:57632400-57635000	Flanking Bivalent TSS/Enh	NHEK	skin
33	chr12:57632600-57634800	Flanking Active TSS	HMEC	breast
34	chr12:57632800-57634400	Active TSS	Right Atrium	heart
35	chr12:57632800-57634600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:57632800-57634600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:57632800-57635000	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr12:57632800-57635400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:57632800-57635400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
40	chr12:57632800-57636400	Bivalent Enhancer	Fetal Heart	heart
41	chr12:57633000-57634200	Bivalent Enhancer	Fetal Lung	lung
42	chr12:57633000-57634400	Active TSS	HSMMtube	muscle
43	chr12:57633200-57634600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:57633200-57634600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
45	chr12:57633200-57634800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:57633200-57634800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:57633200-57634800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
48	chr12:57633200-57634800	Flanking Bivalent TSS/Enh	NH-A	brain
49	chr12:57633200-57635000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
50	chr12:57633400-57634400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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