Variant report

Variant	rs12991768
Chromosome Location	chr2:128146245-128146246
allele	A/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	RUNX3	chr2:128144347-128146478	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:128144343-128146428	GM12891	blood:	n/a	n/a
3	RELA	chr2:128145433-128146520	GM10847	blood:	n/a	n/a
4	STAT5A	chr2:128145671-128146372	GM12878	blood:	n/a	n/a
5	MAX	chr2:128145370-128146614	A549	lung:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
6	MAX	chr2:128144496-128146255	GM12878	blood:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
7	CHD1	chr2:128143649-128147067	IMR90	lung:	n/a	chr2:128145167-128145177
8	REST	chr2:128145625-128146354	A549	lung:	n/a	chr2:128145906-128145915
9	POLR2A	chr2:128145699-128146462	GM12891	blood:	n/a	n/a
10	NRF1	chr2:128144336-128146260	SK-N-SH	brain:	n/a	chr2:128145663-128145674 chr2:128145663-128145677 chr2:128145665-128145674 chr2:128145628-128145639 chr2:128145660-128145674 chr2:128145663-128145674
11	KAP1	chr2:128145883-128146549	HEK293	kidney:	n/a	n/a
12	ATF2	chr2:128145303-128146473	GM12878	blood:	n/a	chr2:128145544-128145558 chr2:128145565-128145579
13	NRF1	chr2:128145424-128146292	GM12878	blood:	n/a	chr2:128145663-128145674 chr2:128145663-128145677 chr2:128145665-128145674 chr2:128145628-128145639 chr2:128145660-128145674 chr2:128145663-128145674
14	EP300	chr2:128144748-128146508	GM12878	blood:	n/a	chr2:128145703-128145719 chr2:128145712-128145728 chr2:128145498-128145507 chr2:128145501-128145517 chr2:128145468-128145484
15	RELA	chr2:128145378-128146483	GM19099	blood:	n/a	n/a
16	TFAP2A	chr2:128144693-128146275	Hela-S3	cervix:	n/a	chr2:128145602-128145617 chr2:128145773-128145788
17	WRNIP1	chr2:128145782-128146599	GM12878	blood:	n/a	n/a
18	RAD21	chr2:128144600-128146451	IMR90	lung:	n/a	chr2:128144843-128144853
19	FOS	chr2:128146005-128146358	MCF10A-Er-Src	breast:	n/a	n/a
20	MBD4	chr2:128145684-128146544	HepG2	liver:	n/a	n/a
21	PML	chr2:128144447-128146442	GM12878	blood:	n/a	n/a
22	BCLAF1	chr2:128144567-128146390	GM12878	blood:	n/a	chr2:128145438-128145451 chr2:128145473-128145486 chr2:128145499-128145508 chr2:128145472-128145485
23	TCF12	chr2:128144476-128146453	A549	lung:	n/a	n/a
24	POLR2A	chr2:128144402-128146409	HepG2	liver:	n/a	n/a
25	MYC	chr2:128145372-128146300	MCF10A-Er-Src	breast:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
26	CHD1	chr2:128144476-128146698	GM12878	blood:	n/a	chr2:128145167-128145177
27	POLR2A	chr2:128144717-128146422	Hela-S3	cervix:	n/a	n/a
28	MYC	chr2:128144598-128146340	K562	blood:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
29	EBF1	chr2:128144520-128147130	GM12878	blood:	n/a	chr2:128145148-128145157 chr2:128145148-128145157 chr2:128147052-128147061
30	POLR2A	chr2:128144374-128146684	HepG2	liver:	n/a	n/a
31	JUND	chr2:128144568-128146498	K562	blood:	n/a	n/a
32	EP300	chr2:128145452-128146284	K562	blood:	n/a	chr2:128145703-128145719 chr2:128145712-128145728 chr2:128145498-128145507 chr2:128145501-128145517 chr2:128145468-128145484
33	POLR2A	chr2:128145694-128146476	GM12891	blood:	n/a	n/a
34	CREB1	chr2:128144340-128146406	HepG2	liver:	n/a	n/a
35	CHD2	chr2:128144621-128146564	GM12878	blood:	n/a	chr2:128145167-128145177
36	CBX3	chr2:128145677-128146326	K562	blood:	n/a	n/a
37	FOXA2	chr2:128146006-128146305	HepG2	liver:	n/a	n/a
38	NFIC	chr2:128145808-128146407	GM12878	blood:	n/a	n/a
39	MXI1	chr2:128144583-128146464	GM12878	blood:	n/a	chr2:128145893-128145902
40	POLR2A	chr2:128144624-128146455	Hela-S3	cervix:	n/a	n/a
41	MAX	chr2:128144534-128146405	NB4	blood:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
42	TFAP2C	chr2:128144674-128146393	Hela-S3	cervix:	n/a	chr2:128145773-128145788
43	RELA	chr2:128144484-128146510	GM18951	blood:	n/a	n/a
44	MAZ	chr2:128144057-128146421	IMR90	lung:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
45	PAX5	chr2:128145198-128146413	GM12878	blood:	n/a	n/a
46	MAZ	chr2:128144576-128146347	K562	blood:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
47	FOXA1	chr2:128144583-128146416	HepG2	liver:	n/a	n/a
48	MTA3	chr2:128144424-128146757	GM12878	blood:	n/a	n/a
49	REST	chr2:128144430-128146248	H1-neurons	neurons:	n/a	chr2:128145442-128145455 chr2:128145906-128145915
50	KAP1	chr2:128145845-128146625	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:128143986..128147167-chr2:128178825..128181533,4	MCF-7	breast:
2	chr2:120435826..120437483-chr2:128143933..128146415,2	MCF-7	breast:
3	chr13:21347604..21348144-chr2:128145436..128146340,2	NB4	blood:
4	chr2:128100404..128103030-chr2:128144500..128146639,3	MCF-7	breast:
5	chr2:128143823..128146469-chr2:128456940..128459025,2	MCF-7	breast:
6	chr2:128050445..128053038-chr2:128144842..128147674,3	K562	blood:
7	chr2:128145128..128146772-chr2:128281228..128284838,3	MCF-7	breast:
8	chr2:128143841..128146885-chr2:128179410..128184717,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PROC-1	chr2:128145948-128146574	NONHSAT074151
2	lnc-PROC-1	chr2:128146190-128146574	NONHSAT074153
3	lnc-PROC-1	chr2:128146043-128146574	NONHSAT074152

Variant related genes	Relation type
ENSG00000236682	TF binding region
MAP3K2	TF binding region
ENSG00000173349	Chromatin interaction
ENSG00000150456	Chromatin interaction
ENSG00000163166	Chromatin interaction
ENSG00000163161	Chromatin interaction
ENSG00000169967	Chromatin interaction
ENSG00000115718	Chromatin interaction
ENSG00000144120	Chromatin interaction
ENSG00000264075	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10803585	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11886231	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11890187	0.91[ASN][1000 genomes]
rs11901355	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12052483	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12463451	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12465955	0.80[ASN][1000 genomes]
rs12477214	0.92[ASN][1000 genomes]
rs12479003	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12622436	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12989081	0.96[ASN][1000 genomes]
rs12989154	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12991062	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13026597	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13026611	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13029237	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1566823	0.82[ASN][1000 genomes]
rs17015199	0.91[ASN][1000 genomes]
rs1799808	0.85[EUR][1000 genomes]
rs1850689	0.96[ASN][1000 genomes]
rs2069924	0.84[EUR][1000 genomes]
rs2069931	0.82[EUR][1000 genomes]
rs2090574	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2174270	0.80[ASN][1000 genomes]
rs2276583	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2896980	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34832797	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35293119	0.96[ASN][1000 genomes]
rs3768866	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150407	0.86[ASN][1000 genomes]
rs4150441	0.82[ASN][1000 genomes]
rs4150454	0.83[ASN][1000 genomes]
rs4150477	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4150495	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4150496	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4233583	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4233584	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4497825	0.87[ASN][1000 genomes]
rs4662575	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4662578	0.91[ASN][1000 genomes]
rs4662580	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4662717	0.81[ASN][1000 genomes]
rs4662722	0.92[ASN][1000 genomes]
rs4662725	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55905117	0.81[ASN][1000 genomes]
rs55998967	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59566504	0.87[ASN][1000 genomes]
rs62157549	0.91[ASN][1000 genomes]
rs62157555	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62160261	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710535	0.82[EUR][1000 genomes]
rs6731176	0.91[ASN][1000 genomes]
rs6732279	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6761447	0.91[ASN][1000 genomes]
rs7568261	0.95[ASN][1000 genomes]
rs7580658	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587639	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7589451	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867304	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9636237	0.91[ASN][1000 genomes]
rs9789510	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3346398	chr2:128143907-128146455	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3327412	chr2:128144082-128146880	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128144200-128146600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:128144200-128146600	Active TSS	Colonic Mucosa	Colon
3	chr2:128144400-128146400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:128144800-128146400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:128144800-128146400	Active TSS	Rectal Smooth Muscle	rectum
6	chr2:128145800-128146400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:128145800-128146400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:128145800-128146400	Flanking Active TSS	Primary B cells from peripheral blood	blood
9	chr2:128145800-128146400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:128145800-128146400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr2:128145800-128146400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:128145800-128146400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:128145800-128146400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr2:128145800-128146400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:128145800-128146400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr2:128145800-128146400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:128145800-128146400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:128145800-128146400	Flanking Active TSS	Fetal Intestine Small	intestine
19	chr2:128145800-128146400	Flanking Active TSS	Stomach Mucosa	stomach
20	chr2:128145800-128146400	Flanking Active TSS	Thymus	Thymus
21	chr2:128145800-128146400	Flanking Active TSS	Dnd41	blood
22	chr2:128145800-128146400	Flanking Bivalent TSS/Enh	HepG2	liver
23	chr2:128145800-128146400	Flanking Active TSS	HMEC	breast
24	chr2:128145800-128146400	Flanking Active TSS	NH-A	brain
25	chr2:128145800-128146400	Flanking Active TSS	NHEK	skin
26	chr2:128145800-128146600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:128145800-128146600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:128145800-128146600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr2:128145800-128146600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:128145800-128146600	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr2:128145800-128146600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr2:128145800-128146600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr2:128145800-128146600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr2:128145800-128146600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:128145800-128146600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:128145800-128146600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr2:128145800-128146600	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr2:128145800-128146600	Flanking Active TSS	Fetal Lung	lung
39	chr2:128145800-128146600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr2:128145800-128146600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr2:128145800-128146600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr2:128145800-128146600	Flanking Active TSS	Osteobl	bone
43	chr2:128145800-128146800	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr2:128145800-128146800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:128145800-128146800	Flanking Active TSS	Hela-S3	cervix
46	chr2:128145800-128148400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr2:128146000-128146400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr2:128146000-128146400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:128146000-128146400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr2:128146000-128146400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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