Variant report

Variant	rs12092479
Chromosome Location	chr1:154972984-154972985
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	chr1:154972843-154974125	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr1:154972384-154974658	HepG2	liver:	n/a	chr1:154972834-154972848 chr1:154972469-154972478
3	POLR2A	chr1:154972079-154973082	HepG2	liver:	n/a	n/a
4	MXI1	chr1:154972208-154974976	HepG2	liver:	n/a	n/a
5	CTCF	chr1:154972840-154972990	AG04449	skin:	n/a	n/a
6	POLR2A	chr1:154972133-154973073	PANC-1	pancreas:	n/a	n/a
7	SMARCB1	chr1:154972832-154974688	Hela-S3	cervix:	n/a	chr1:154973582-154973591
8	UBTF	chr1:154972284-154974974	K562	blood:	n/a	n/a
9	POLR2A	chr1:154972087-154974866	MCF-7	breast:	n/a	n/a
10	MAZ	chr1:154972914-154977198	Hela-S3	cervix:	n/a	chr1:154975177-154975187 chr1:154976774-154976783 chr1:154974589-154974599 chr1:154974425-154974435 chr1:154975005-154975015 chr1:154976366-154976376 chr1:154975835-154975845 chr1:154977177-154977186 chr1:154974633-154974643 chr1:154973886-154973896 chr1:154974592-154974602
11	MYC	chr1:154972917-154973085	MCF-7	breast:	n/a	n/a
12	PML	chr1:154971348-154974989	GM12878	blood:	n/a	chr1:154971803-154971811
13	POLR2A	chr1:154972814-154973848	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr1:154971367-154973909	GM15510	blood:	n/a	n/a
15	GATA3	chr1:154972918-154977134	A549	lung:	n/a	chr1:154976773-154976782 chr1:154973839-154973847
16	HCFC1	chr1:154972249-154973919	K562	blood:	n/a	n/a
17	POLR2A	chr1:154972746-154973090	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr1:154972882-154973087	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:154972321-154973104	HepG2	liver:	n/a	n/a
20	RUNX3	chr1:154971400-154973069	GM12878	blood:	n/a	chr1:154972079-154972094
21	POLR2A	chr1:154971651-154974970	Hela-S3	cervix:	n/a	n/a
22	JUND	chr1:154972265-154974911	K562	blood:	n/a	chr1:154973580-154973591 chr1:154973582-154973590 chr1:154973343-154973357 chr1:154973280-154973294 chr1:154973580-154973592 chr1:154974688-154974697 chr1:154973581-154973591 chr1:154973396-154973410
23	HEY1	chr1:154972661-154973088	HepG2	liver:	n/a	n/a
24	YY1	chr1:154972972-154973969	HepG2	liver:	n/a	chr1:154973694-154973708 chr1:154972975-154972984
25	POLR2A	chr1:154971547-154973078	K562	blood:	n/a	n/a
26	EBF1	chr1:154972427-154973558	GM12878	blood:	n/a	chr1:154972663-154972674
27	MAX	chr1:154971469-154973088	K562	blood:	n/a	chr1:154972358-154972368 chr1:154972358-154972367 chr1:154972358-154972367 chr1:154972692-154972702 chr1:154971524-154971533 chr1:154972356-154972371 chr1:154972074-154972083 chr1:154972359-154972366 chr1:154972357-154972368
28	POLR2A	chr1:154971682-154973931	HEK293	kidney:	n/a	n/a
29	POLR2A	chr1:154971422-154973088	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:154972755-154974730	MCF-7	breast:	n/a	n/a
31	POLR2A	chr1:154972562-154974938	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:154971382-154973080	GM12878	blood:	n/a	n/a
33	HEY1	chr1:154971485-154973090	K562	blood:	n/a	chr1:154971909-154971924
34	POLR2A	chr1:154972904-154973076	Hela-S3	cervix:	n/a	n/a
35	TFAP2C	chr1:154972862-154974869	Hela-S3	cervix:	n/a	chr1:154973517-154973532 chr1:154972999-154973014
36	MYC	chr1:154971588-154973977	K562	blood:	n/a	chr1:154972358-154972368 chr1:154972358-154972367 chr1:154972358-154972367 chr1:154972692-154972702 chr1:154972356-154972371 chr1:154972074-154972083 chr1:154972359-154972366 chr1:154972357-154972368 chr1:154973886-154973896
37	POLR2A	chr1:154971387-154974123	GM12891	blood:	n/a	n/a
38	RELA	chr1:154972270-154974142	GM18951	blood:	n/a	chr1:154973277-154973286 chr1:154973394-154973403 chr1:154973277-154973286 chr1:154973394-154973403
39	POLR2A	chr1:154971396-154974731	GM18505	blood:	n/a	n/a
40	POLR2A	chr1:154972464-154973096	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:154971426-154974922	GM18951	blood:	n/a	n/a
42	POLR2A	chr1:154971491-154974246	HCT-116	colon:	n/a	n/a
43	NFIC	chr1:154972179-154972990	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:154972854-154973055	A549	lung:	n/a	n/a
45	EGR1	chr1:154972075-154975034	HCT-116	colon:	n/a	chr1:154974629-154974642 chr1:154974753-154974766 chr1:154972689-154972702 chr1:154974630-154974640 chr1:154972688-154972703 chr1:154972689-154972702 chr1:154974626-154974640 chr1:154974150-154974163 chr1:154972691-154972701 chr1:154974628-154974643 chr1:154975016-154975029 chr1:154974629-154974642 chr1:154973890-154973914 chr1:154974151-154974161 chr1:154974751-154974761 chr1:154975015-154975030 chr1:154974327-154974340 chr1:154972648-154972662
46	BCL3	chr1:154972744-154974723	A549	lung:	n/a	chr1:154974627-154974636 chr1:154972785-154972794 chr1:154973562-154973575 chr1:154973276-154973285
47	POLR2A	chr1:154972183-154974962	HepG2	liver:	n/a	n/a
48	ZBTB7A	chr1:154971613-154973122	K562	blood:	n/a	chr1:154972176-154972187 chr1:154972217-154972231 chr1:154972096-154972105
49	MAX	chr1:154972047-154975108	HepG2	liver:	n/a	chr1:154972358-154972368 chr1:154972358-154972367 chr1:154974589-154974599 chr1:154974425-154974435 chr1:154972358-154972367 chr1:154972692-154972702 chr1:154975005-154975015 chr1:154972356-154972371 chr1:154972074-154972083 chr1:154972359-154972366 chr1:154972357-154972368 chr1:154974633-154974643 chr1:154973886-154973896 chr1:154974592-154974602
50	RCOR1	chr1:154972829-154974933	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:154972965-154973015	HIPEpiC	eye:	n/a
2	chr1:154972965-154973015	HL-60	blood:	n/a
3	chr1:154972965-154973015	AG10803	skin:	n/a
4	chr1:154972965-154973015	HCT-116	colon:	n/a
5	chr1:154972965-154973015	H1-hESC	embryonic stem cell:	embryo
6	chr1:154972965-154973015	NH-A	brain:	n/a
7	chr1:154972965-154973015	HCPEpiC	choroid plexus:	n/a
8	chr1:154972965-154973015	ProgFib	skin:	n/a
9	chr1:154972965-154973015	LNCaP	prostate:	n/a
10	chr1:154972965-154973015	HCF	heart:	n/a
11	chr1:154972965-154973015	HepG2	liver:	n/a
12	chr1:154972965-154973015	U87	brain:	n/a
13	chr1:154972965-154973015	GM19239	blood:	n/a
14	chr1:154972965-154973015	ovcar-3	ovarian:	n/a
15	chr1:154972965-154973015	SK-N-SH	brain:	n/a
16	chr1:154972965-154973015	K562	blood:	n/a
17	chr1:154972965-154973015	MCF10A-Er-Src	breast:	n/a
18	chr1:154972965-154973015	AG09319	gingival:	n/a
19	chr1:154972965-154973015	SK-N-MC	brain:	n/a
20	chr1:154972965-154973015	Hepatocyte	liver:	n/a
21	chr1:154972965-154973015	T-47D	breast:	n/a
22	chr1:154972965-154973015	MCF-7	breast:	n/a
23	chr1:154972965-154973015	PANC-1	pancreas:	n/a
24	chr1:154972965-154973015	HAEpiC	amniotic membrane:	n/a
25	chr1:154972965-154973015	NHBE	bronchial:	n/a
26	chr1:154972965-154973015	Hela-S3	cervix:	n/a
27	chr1:154972965-154973015	HUVEC	blood vessel:	n/a
28	chr1:154972965-154973015	SK-N-SH_RA	brain:	n/a
29	chr1:154972965-154973015	HMEC	breast:	n/a
30	chr1:154972965-154973015	BJ	skin:	n/a
31	chr1:154972965-154973015	AG04450	lung:	fetal
32	chr1:154972965-154973015	HPAEpiC	pulmonary alveolar:	n/a
33	chr1:154972965-154973015	BE2_C	brain:	n/a
34	chr1:154972965-154973015	Caco-2	colon:	n/a
35	chr1:154972965-154973015	A549	lung:	n/a
36	chr1:154972965-154973015	GM12892	blood:	n/a
37	chr1:154972965-154973015	NHDF-neo	bronchial:	n/a
38	chr1:154972965-154973015	GM06990	blood:	n/a
39	chr1:154972965-154973015	PFSK-1	brain:	n/a
40	chr1:154972965-154973015	GM12891	blood:	n/a
41	chr1:154972965-154973015	AG04449	skin:	fetal
42	chr1:154972965-154973015	NB4	blood:	n/a
43	chr1:154972965-154973015	HNPCEpiC	eye:	n/a
44	chr1:154972965-154973015	HCM	heart:	n/a
45	chr1:154972965-154973015	AG09309	skin:	n/a
46	chr1:154972965-154973015	PrEC	prostate:	n/a
47	chr1:154972965-154973015	IMR90	lung:	fetal
48	chr1:154972965-154973015	SKMC	muscle:	n/a
49	chr1:154972965-154973015	HEK293	kidney:	embryo
50	chr1:154972965-154973015	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154972444..154977644-chr1:155020190..155026477,10	K562	blood:
2	chr1:154972817..154976051-chr1:155001512..155004606,5	MCF-7	breast:
3	chr1:154972933..154973551-chr20:61293187..61293687,2	NB4	blood:
4	chr1:154968418..154978887-chr1:155021582..155027516,28	MCF-7	breast:
5	chr1:154972344..154977668-chr1:155022111..155025561,8	K562	blood:
6	chr1:154972832..154974574-chr1:155014672..155017618,2	K562	blood:
7	chr1:154897327..154899554-chr1:154972284..154973905,2	K562	blood:
8	chr1:154971529..154973537-chr1:155057586..155059382,2	K562	blood:
9	chr1:154971773..154974772-chr1:155107773..155110991,3	K562	blood:
10	chr1:154972561..154974710-chr1:155165373..155167447,2	MCF-7	breast:
11	chr1:154967268..154977621-chr1:155049775..155059069,28	MCF-7	breast:
12	chr1:153963267..153965120-chr1:154971988..154974944,2	K562	blood:
13	chr1:107598824..107600946-chr1:154972687..154974948,2	MCF-7	breast:
14	chr1:154968645..154978750-chr1:155013210..155021460,25	MCF-7	breast:
15	chr1:154971203..154978007-chr1:155093683..155103687,24	MCF-7	breast:
16	chr1:154971672..154974810-chr1:155055018..155057601,4	K562	blood:
17	chr1:154970467..154977420-chr1:155052491..155060843,19	MCF-7	breast:
18	chr1:154972799..154973489-chr8:99305948..99306767,2	HCT-116	colon:
19	chr1:154969072..154977664-chr1:155030052..155039846,22	MCF-7	breast:
20	chr1:154970938..154973670-chr1:155108868..155110431,2	MCF-7	breast:
21	chr1:154971009..154978300-chr1:155033602..155036845,7	K562	blood:
22	chr1:154972330..154977027-chr1:155049641..155053541,6	K562	blood:
23	chr1:154971124..154975632-chr1:155030158..155034057,4	K562	blood:
24	chr1:154970902..154974012-chr1:155057882..155061040,3	K562	blood:
25	chr1:154972838..154974004-chr1:154989871..154990584,3	Hela-S3	cervix:
26	chr1:154892548..154895461-chr1:154971772..154973336,2	K562	blood:
27	chr1:154971801..154975044-chr1:155161856..155165881,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCST2-2	chr1:154969743-154973116	NONHSAT006664

Variant related genes	Relation type
ZBTB7B	TF binding region
ZBTB7B	CpG island
ENSG00000251246	Chromatin interaction
ENSG00000104361	Chromatin interaction
ENSG00000231064	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000163354	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000198890	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12059540	1.00[MEX][hapmap]
rs12064595	1.00[MEX][hapmap]
rs12078687	1.00[MEX][hapmap]
rs2232635	1.00[MEX][hapmap]
rs9236	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	575 gene(s)	inside rSNPs	diseases
2	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription 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
4	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 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	chr1:154969800-154974800	Bivalent Enhancer	Dnd41	blood
2	chr1:154971000-154973200	Weak transcription	Gastric	stomach
3	chr1:154971400-154973000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr1:154971400-154973000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr1:154971400-154973000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:154971400-154973000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:154971400-154973000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:154971400-154973000	Flanking Active TSS	Fetal Intestine Large	intestine
9	chr1:154971400-154973000	Flanking Active TSS	Fetal Muscle Trunk	muscle
10	chr1:154971400-154973000	Flanking Active TSS	Fetal Muscle Leg	muscle
11	chr1:154971400-154973000	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr1:154971400-154973800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:154971400-154974200	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr1:154971400-154974200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr1:154971400-154974200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:154971400-154974600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:154971400-154974600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:154971400-154976600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:154971400-154976800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:154971400-154976800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:154971400-154977000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr1:154971600-154973000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:154971600-154973000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr1:154971600-154973000	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr1:154971600-154973000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:154971600-154973000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr1:154971600-154973000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:154971600-154973000	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr1:154971600-154973000	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr1:154971600-154973000	Flanking Active TSS	Colonic Mucosa	Colon
31	chr1:154971600-154973000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr1:154971600-154973000	Flanking Active TSS	Fetal Intestine Small	intestine
33	chr1:154971600-154973000	Flanking Active TSS	A549	lung
34	chr1:154971600-154973000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr1:154971600-154973000	Flanking Active TSS	Osteobl	bone
36	chr1:154971600-154973200	Enhancers	Spleen	Spleen
37	chr1:154971600-154974200	Flanking Active TSS	Placenta	Placenta
38	chr1:154971600-154976600	Active TSS	Right Atrium	heart
39	chr1:154971600-154976800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:154971600-154976800	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:154971600-154976800	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr1:154971600-154976800	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:154971600-154976800	Active TSS	Ovary	ovary
44	chr1:154971600-154977200	Active TSS	Aorta	Aorta
45	chr1:154971600-154977400	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr1:154971800-154973200	Enhancers	Lung	lung
47	chr1:154971800-154973400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:154971800-154973600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:154971800-154973800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr1:154971800-154973800	Active TSS	GM12878-XiMat	blood

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