Variant report

Variant	rs2541136
Chromosome Location	chr12:11801640-11801641
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	POLR2A	chr12:11801536-11802609	PBDE	blood:	n/a	n/a
2	E2F6	chr12:11801556-11802286	A549	lung:	n/a	n/a
3	POLR2A	chr12:11801618-11802103	HepG2	liver:	n/a	n/a
4	ZMIZ1	chr12:11801633-11802659	K562	blood:	n/a	n/a
5	MAX	chr12:11801567-11802319	K562	blood:	n/a	chr12:11801906-11801915
6	CTCF	chr12:11801500-11801650	HCPEpiC	choroid plexus:	n/a	n/a
7	CEBPB	chr12:11801552-11802043	MCF-7	breast:	n/a	n/a
8	TEAD4	chr12:11801566-11802856	ECC-1	luminal epithelium:	n/a	n/a
9	HEY1	chr12:11801564-11802719	K562	blood:	n/a	chr12:11801983-11801998 chr12:11801972-11801987 chr12:11801981-11801996
10	NFIC	chr12:11801470-11802727	ECC-1	luminal epithelium:	n/a	n/a
11	CTCF	chr12:11801560-11801710	HCM	heart:	n/a	n/a
12	SP1	chr12:11801394-11802928	HCT-116	colon:	n/a	chr12:11802851-11802861
13	SIX5	chr12:11801602-11801849	A549	lung:	n/a	n/a
14	ELF1	chr12:11801505-11802414	MCF-7	breast:	n/a	chr12:11802134-11802147 chr12:11802136-11802147 chr12:11801882-11801894
15	BACH1	chr12:11801575-11803181	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr12:11801561-11802316	K562	blood:	n/a	chr12:11801906-11801915
17	WRNIP1	chr12:11801572-11802321	GM12878	blood:	n/a	n/a
18	MAX	chr12:11801503-11802901	HepG2	liver:	n/a	chr12:11801906-11801915
19	POLR2A	chr12:11801631-11802402	HepG2	liver:	n/a	n/a
20	HEY1	chr12:11801571-11802819	HepG2	liver:	n/a	chr12:11801983-11801998 chr12:11801972-11801987 chr12:11801981-11801996
21	SP1	chr12:11801433-11802855	A549	lung:	n/a	n/a
22	ARID3A	chr12:11801464-11802268	K562	blood:	n/a	n/a
23	RELA	chr12:11801585-11803223	GM18951	blood:	n/a	n/a
24	MYC	chr12:11801266-11804056	K562	blood:	n/a	chr12:11801906-11801915
25	CTCF	chr12:11801580-11801730	AG09309	skin:	n/a	n/a
26	PBX3	chr12:11801514-11802869	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr12:11801520-11801670	HCFaa	heart:	n/a	n/a
28	MAZ	chr12:11801601-11803424	K562	blood:	n/a	chr12:11801906-11801915
29	ELF1	chr12:11801511-11802432	SK-N-SH	brain:	n/a	chr12:11802134-11802147 chr12:11802136-11802147 chr12:11801882-11801894
30	JUND	chr12:11801637-11801928	H1-hESC	embryonic stem cell:	n/a	n/a
31	FOS	chr12:11801557-11802296	MCF10A-Er-Src	breast:	n/a	n/a
32	CTCF	chr12:11801580-11801730	HCPEpiC	choroid plexus:	n/a	n/a
33	CHD1	chr12:11801617-11802311	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAFK	chr12:11801589-11801789	K562	blood:	n/a	n/a
35	POLR2A	chr12:11801595-11806717	GM18951	blood:	n/a	n/a
36	POLR2A	chr12:11801547-11802419	SK-N-MC	brain:	n/a	n/a
37	MYC	chr12:11801640-11802692	K562	blood:	n/a	chr12:11801906-11801915
38	TCF7L2	chr12:11801567-11803228	HCT-116	colon:	n/a	n/a
39	RELA	chr12:11801569-11803269	GM15510	blood:	n/a	n/a
40	CTCF	chr12:11801560-11801710	AG04449	skin:	n/a	n/a
41	SMC3	chr12:11801516-11802708	Hela-S3	cervix:	n/a	chr12:11802566-11802573
42	ELF1	chr12:11801456-11802432	HCT-116	colon:	n/a	chr12:11802134-11802147 chr12:11802136-11802147 chr12:11801882-11801894
43	TAF1	chr12:11801599-11802762	H1-neurons	neurons:	n/a	n/a
44	ZNF384	chr12:11801573-11801785	K562	blood:	n/a	n/a
45	HDAC2	chr12:11801519-11802382	H1-hESC	embryonic stem cell:	n/a	chr12:11802133-11802147
46	POLR2A	chr12:11801569-11802754	GM12892	blood:	n/a	n/a
47	MAX	chr12:11801558-11802696	NB4	blood:	n/a	chr12:11801906-11801915
48	CEBPB	chr12:11801528-11802253	A549	lung:	n/a	n/a
49	POLR2A	chr12:11801483-11802414	GM12891	blood:	n/a	n/a
50	NANOG	chr12:11801575-11801849	H1-hESC	embryonic stem cell:	n/a	chr12:11801617-11801626

No.	Distal block	Cell Line	Cell type
1	chr12:11800508..11802179-chr12:11860722..11862273,2	MCF-7	breast:
2	chr12:11800455..11804262-chr12:12036773..12041762,7	MCF-7	breast:
3	chr12:11801531..11802163-chr17:73775414..73776004,2	Hela-S3	cervix:
4	chr12:11786072..11788465-chr12:11800287..11802406,2	K562	blood:
5	chr12:11784813..11787611-chr12:11800177..11801948,2	MCF-7	breast:
6	chr12:11800032..11801851-chr12:11845652..11848182,2	MCF-7	breast:
7	chr12:11801548..11802214-chr5:134209797..134210407,2	Hela-S3	cervix:
8	chr12:11801597..11802471-chr16:4475860..4476434,2	Hela-S3	cervix:
9	chr12:11801638..11802342-chr8:131054390..131055145,2	Hela-S3	cervix:
10	chr12:11800154..11802196-chr12:11905804..11907326,2	MCF-7	breast:
11	chr12:11799547..11802655-chr12:12030358..12032726,3	MCF-7	breast:
12	chr12:11800191..11804184-chr12:12034563..12039946,8	MCF-7	breast:

Variant related genes	Relation type
ETV6	TF binding region
ENSG00000139083	Chromatin interaction
ENSG00000113621	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000103423	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11833038	1.00[AMR][1000 genomes]
rs1861485	1.00[AMR][1000 genomes]
rs2541120	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2541134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2724591	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2724607	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2724647	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2856312	1.00[AMR][1000 genomes]
rs2856318	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 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	chr12:11801000-11801800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr12:11801000-11802000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:11801000-11804000	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr12:11801000-11804600	Active TSS	Fetal Kidney	kidney
5	chr12:11801000-11804800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:11801000-11805200	Active TSS	Stomach Smooth Muscle	stomach
7	chr12:11801200-11803800	Active TSS	Placenta Amnion	Placenta Amnion
8	chr12:11801200-11804800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:11801200-11805200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:11801200-11805200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:11801200-11805200	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr12:11801200-11805600	Active TSS	Fetal Muscle Trunk	muscle
13	chr12:11801200-11805800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:11801200-11806000	Active TSS	GM12878-XiMat	blood
15	chr12:11801400-11801800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:11801400-11801800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:11801400-11801800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr12:11801400-11801800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr12:11801400-11801800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr12:11801400-11801800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:11801400-11801800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr12:11801400-11801800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr12:11801400-11801800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:11801400-11801800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:11801400-11801800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:11801400-11801800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr12:11801400-11801800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:11801400-11801800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:11801400-11801800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:11801400-11801800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr12:11801400-11801800	Flanking Active TSS	Liver	Liver
32	chr12:11801400-11801800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr12:11801400-11801800	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr12:11801400-11801800	Flanking Active TSS	Placenta	Placenta
35	chr12:11801400-11801800	Flanking Active TSS	Fetal Thymus	thymus
36	chr12:11801400-11801800	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr12:11801400-11801800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr12:11801400-11801800	Flanking Active TSS	Dnd41	blood
39	chr12:11801400-11801800	Flanking Active TSS	HUVEC	blood vessel
40	chr12:11801400-11801800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr12:11801400-11801800	Flanking Active TSS	NH-A	brain
42	chr12:11801400-11801800	Flanking Active TSS	NHEK	skin
43	chr12:11801400-11802000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr12:11801400-11802000	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr12:11801400-11802000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr12:11801400-11802000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:11801400-11802000	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr12:11801400-11803600	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr12:11801400-11803600	Active TSS	Primary T cells from cord blood	blood
50	chr12:11801400-11803600	Active TSS	HepG2	liver

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