Variant report

Variant	rs12991441
Chromosome Location	chr2:172750262-172750263
allele	C/G
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	SIN3AK20	chr2:172750223-172751069	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr2:172750125-172751381	K562	blood:	n/a	chr2:172750674-172750685 chr2:172750673-172750686
3	CEBPB	chr2:172750220-172750851	HepG2	liver:	n/a	chr2:172750674-172750685 chr2:172750673-172750686
4	RUNX3	chr2:172750103-172751272	GM12878	blood:	n/a	n/a
5	SIN3A	chr2:172750248-172751382	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:172750234-172751128	GM12891	blood:	n/a	n/a
7	MAX	chr2:172750261-172751384	HepG2	liver:	n/a	chr2:172750865-172750874
8	POLR2A	chr2:172750166-172751313	GM19099	blood:	n/a	n/a
9	KAP1	chr2:172749956-172751411	U2OS	brain:	n/a	n/a
10	CEBPB	chr2:172750150-172751140	HepG2	liver:	n/a	chr2:172750674-172750685 chr2:172750673-172750686
11	RELA	chr2:172750051-172751297	GM12891	blood:	n/a	chr2:172751024-172751033 chr2:172751024-172751033
12	TEAD4	chr2:172749785-172751436	K562	blood:	n/a	n/a
13	RELA	chr2:172749918-172751374	GM10847	blood:	n/a	chr2:172751024-172751033 chr2:172751024-172751033
14	POLR2A	chr2:172749790-172751560	GM12891	blood:	n/a	n/a
15	POLR2A	chr2:172750261-172751114	HCT-116	colon:	n/a	n/a
16	PML	chr2:172750198-172751176	K562	blood:	n/a	n/a
17	CEBPB	chr2:172750117-172750956	H1-hESC	embryonic stem cell:	n/a	chr2:172750674-172750685 chr2:172750673-172750686
18	POLR2A	chr2:172750242-172751219	GM19193	blood:	n/a	n/a
19	POLR2A	chr2:172750160-172751295	HUVEC	blood vessel:	n/a	n/a
20	BCL3	chr2:172750129-172750590	A549	lung:	n/a	chr2:172750443-172750452 chr2:172750574-172750587
21	STAT3	chr2:172750172-172750309	MCF10A-Er-Src	breast:	n/a	n/a
22	SPI1	chr2:172750131-172750925	HL-60	blood:	n/a	n/a
23	CEBPB	chr2:172750166-172750981	GM12878	blood:	n/a	chr2:172750674-172750685 chr2:172750673-172750686
24	YY1	chr2:172750241-172751106	GM12892	blood:	n/a	chr2:172750823-172750837 chr2:172750716-172750728
25	POLR2A	chr2:172750099-172751231	GM18505	blood:	n/a	n/a
26	NR2F2	chr2:172750040-172751593	K562	blood:	n/a	n/a
27	CEBPB	chr2:172750132-172751232	Hela-S3	cervix:	n/a	chr2:172750674-172750685 chr2:172750673-172750686
28	MAX	chr2:172750180-172751277	K562	blood:	n/a	chr2:172750865-172750874
29	MAX	chr2:172750227-172751204	NB4	blood:	n/a	chr2:172750865-172750874
30	MYC	chr2:172749951-172751192	NB4	blood:	n/a	chr2:172750865-172750874
31	TEAD4	chr2:172750201-172751337	HepG2	liver:	n/a	n/a
32	SPI1	chr2:172750203-172750600	HL-60	blood:	n/a	n/a
33	ETS1	chr2:172750217-172751167	K562	blood:	n/a	chr2:172750522-172750533 chr2:172750388-172750395 chr2:172750384-172750395 chr2:172750382-172750396
34	MYC	chr2:172750058-172750393	MCF10A-Er-Src	breast:	n/a	n/a
35	MTA3	chr2:172749830-172750739	GM12878	blood:	n/a	n/a
36	FOXA1	chr2:172750198-172751101	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:172750114-172751314	K562	blood:	n/a	n/a
38	CEBPB	chr2:172750158-172751205	MCF-7	breast:	n/a	chr2:172750674-172750685 chr2:172750673-172750686
39	CEBPB	chr2:172750103-172750863	ECC-1	luminal epithelium:	n/a	chr2:172750674-172750685 chr2:172750673-172750686
40	POLR2A	chr2:172750163-172751570	MCF10A-Er-Src	breast:	n/a	n/a
41	PML	chr2:172750162-172751299	K562	blood:	n/a	n/a
42	RELA	chr2:172750207-172751196	GM15510	blood:	n/a	chr2:172751024-172751033 chr2:172751024-172751033
43	POLR2A	chr2:172749979-172751365	GM12878	blood:	n/a	n/a
44	POLR2A	chr2:172750252-172751228	K562	blood:	n/a	n/a
45	RFX5	chr2:172750228-172751230	Hela-S3	cervix:	n/a	chr2:172750998-172751015
46	MAX	chr2:172750146-172751476	A549	lung:	n/a	chr2:172750865-172750874
47	POLR2A	chr2:172750032-172751211	GM12891	blood:	n/a	n/a
48	POLR2A	chr2:172750204-172751231	H1-neurons	neurons:	n/a	n/a
49	NFIC	chr2:172749969-172751131	GM12878	blood:	n/a	n/a
50	TAL1	chr2:172750230-172751023	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:172749328..172751742-chr2:172775594..172779310,3	MCF-7	breast:
2	chr2:172749212..172752099-chr2:172863500..172865923,3	MCF-7	breast:
3	chr2:172749065..172752809-chr2:172776821..172780584,7	K562	blood:
4	chr2:172749345..172750892-chr2:172948772..172951061,2	MCF-7	breast:
5	chr2:172749385..172752362-chr2:172779098..172783248,3	MCF-7	breast:
6	chr2:172289011..172290991-chr2:172749560..172752051,2	K562	blood:
7	chr2:172543765..172545467-chr2:172749369..172751686,2	MCF-7	breast:

Variant related genes	Relation type
SLC25A12	TF binding region
ENSG00000077380	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000128708	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11673831	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11675404	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11675891	0.82[AMR][1000 genomes]
rs11691301	0.90[ASN][1000 genomes]
rs13016580	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13017695	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13021138	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13024662	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554259	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17427311	0.81[AMR][1000 genomes]
rs17427473	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17499306	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17499502	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17848721	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1996424	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2138349	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2357062	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34108287	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34221876	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34632749	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34962243	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35162284	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3770459	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62182397	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62182402	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62184174	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74173119	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1006214	chr2:172691689-172754296	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
3	nsv536036	chr2:172691689-172754296	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv536037	chr2:172745597-172780616	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172748000-172751600	Active TSS	GM12878-XiMat	blood
2	chr2:172748200-172751000	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr2:172749600-172750400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:172749600-172750400	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr2:172749600-172750400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr2:172749600-172750400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:172749600-172750400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:172749600-172750400	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr2:172749600-172750400	Flanking Active TSS	Fetal Brain Female	brain
10	chr2:172749600-172750400	Flanking Active TSS	Fetal Lung	lung
11	chr2:172749600-172750400	Flanking Active TSS	Hela-S3	cervix
12	chr2:172749600-172750400	Flanking Active TSS	NHEK	skin
13	chr2:172749600-172750400	Flanking Active TSS	Osteobl	bone
14	chr2:172749600-172750600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:172749600-172750600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:172749600-172750600	Flanking Active TSS	Brain Angular Gyrus	brain
17	chr2:172749600-172751200	Active TSS	Left Ventricle	heart
18	chr2:172749600-172751400	Active TSS	Ovary	ovary
19	chr2:172749600-172751400	Active TSS	Psoas Muscle	Psoas
20	chr2:172749600-172751400	Active TSS	Right Atrium	heart
21	chr2:172749600-172751400	Active TSS	Right Ventricle	heart
22	chr2:172749600-172751600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:172749600-172751800	Active TSS	Stomach Smooth Muscle	stomach
24	chr2:172749800-172750400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr2:172749800-172750400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr2:172749800-172750400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:172749800-172750400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr2:172749800-172750400	Flanking Active TSS	Fetal Thymus	thymus
29	chr2:172749800-172750400	Flanking Active TSS	HUVEC	blood vessel
30	chr2:172749800-172750600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr2:172749800-172750600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr2:172749800-172750600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr2:172749800-172750600	Flanking Active TSS	Liver	Liver
34	chr2:172749800-172750600	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr2:172749800-172750600	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr2:172749800-172751200	Active TSS	Fetal Heart	heart
37	chr2:172749800-172751200	Active TSS	Thymus	Thymus
38	chr2:172749800-172751400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:172749800-172751400	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr2:172749800-172751400	Active TSS	Colonic Mucosa	Colon
41	chr2:172749800-172751400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr2:172749800-172751400	Active TSS	HSMMtube	muscle
43	chr2:172749800-172751600	Active TSS	HSMM	muscle
44	chr2:172750000-172750400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr2:172750000-172750400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr2:172750000-172750400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr2:172750000-172750400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr2:172750000-172750400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:172750000-172750400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr2:172750000-172750400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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