Variant report

Variant	rs73280729
Chromosome Location	chr12:46664108-46664109
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	POLR2A	chr12:46660289-46664356	GM12878	blood:	n/a	n/a
2	REST	chr12:46659510-46664275	H1-neurons	neurons:	n/a	chr12:46659623-46659636 chr12:46662267-46662280 chr12:46663282-46663300 chr12:46661825-46661835 chr12:46662267-46662280 chr12:46663275-46663288 chr12:46660714-46660728
3	MAX	chr12:46662419-46664133	H1-hESC	embryonic stem cell:	n/a	chr12:46663629-46663639 chr12:46663630-46663640 chr12:46663626-46663641 chr12:46663631-46663640 chr12:46662836-46662846 chr12:46662583-46662592 chr12:46663628-46663643 chr12:46663630-46663639 chr12:46663385-46663395
4	NFATC1	chr12:46663592-46664163	GM12878	blood:	n/a	n/a
5	RELA	chr12:46661799-46664251	GM10847	blood:	n/a	chr12:46663839-46663848 chr12:46663839-46663848
6	POLR2A	chr12:46661859-46664222	GM12892	blood:	n/a	n/a
7	RELA	chr12:46660632-46664260	GM12891	blood:	n/a	chr12:46663839-46663848 chr12:46663839-46663848
8	FOS	chr12:46663830-46664132	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:46660926-46664389	GM12891	blood:	n/a	n/a
10	POLR2A	chr12:46660578-46664376	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:46660499-46664406	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:46660451-46664243	GM12892	blood:	n/a	n/a
13	TBP	chr12:46663675-46664188	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:46660491-46664182	GM12891	blood:	n/a	n/a
15	RUNX3	chr12:46661591-46664256	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:46658963-46665919	GM12891	blood:	n/a	n/a
17	MXI1	chr12:46660240-46664296	GM12878	blood:	n/a	chr12:46663631-46663640 chr12:46663629-46663638
18	POLR2A	chr12:46660692-46664152	GM15510	blood:	n/a	n/a
19	POLR2A	chr12:46658953-46664378	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:46660663-46664322	GM18951	blood:	n/a	n/a
21	FOS	chr12:46663800-46664128	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr12:46660317-46664255	GM18505	blood:	n/a	n/a
23	POLR2A	chr12:46660703-46664160	Raji	blood:	n/a	n/a
24	CHD1	chr12:46659151-46664124	GM12878	blood:	n/a	chr12:46661713-46661723
25	POLR2A	chr12:46660213-46664302	GM12892	blood:	n/a	n/a
26	POLR2A	chr12:46662130-46664122	GM12891	blood:	n/a	n/a
27	SIN3A	chr12:46660196-46664281	H1-hESC	embryonic stem cell:	n/a	chr12:46661130-46661143 chr12:46663278-46663291 chr12:46663471-46663480 chr12:46663935-46663945 chr12:46660715-46660729 chr12:46663288-46663301 chr12:46663295-46663304 chr12:46663631-46663640
28	POLR2A	chr12:46660109-46664125	GM12892	blood:	n/a	n/a
29	STAT5A	chr12:46660586-46664232	GM12878	blood:	n/a	chr12:46664203-46664214 chr12:46662940-46662952 chr12:46662934-46662946 chr12:46661241-46661249 chr12:46662275-46662287 chr12:46661964-46661972
30	E2F6	chr12:46662067-46664125	H1-hESC	embryonic stem cell:	n/a	chr12:46663365-46663380 chr12:46663747-46663761 chr12:46663393-46663402 chr12:46663364-46663376 chr12:46663008-46663017 chr12:46663751-46663758 chr12:46663751-46663758 chr12:46663751-46663758
31	ATF2	chr12:46663320-46664161	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:46660618-46664192	GM18526	blood:	n/a	n/a
33	MTA3	chr12:46660063-46664396	GM12878	blood:	n/a	n/a
34	NFIC	chr12:46663468-46664392	GM12878	blood:	n/a	n/a
35	MXI1	chr12:46659809-46664190	SK-N-SH	brain:	n/a	chr12:46663631-46663640 chr12:46663629-46663638
36	MAX	chr12:46660250-46664385	NB4	blood:	n/a	chr12:46663629-46663639 chr12:46663630-46663640 chr12:46663626-46663641 chr12:46662114-46662123 chr12:46663631-46663640 chr12:46661716-46661726 chr12:46662836-46662846 chr12:46662583-46662592 chr12:46663628-46663643 chr12:46663630-46663639 chr12:46663385-46663395
37	POLR2A	chr12:46658950-46664317	GM12878	blood:	n/a	n/a
38	CHD1	chr12:46663102-46664367	H1-hESC	embryonic stem cell:	n/a	n/a
39	FOS	chr12:46663822-46664148	MCF10A-Er-Src	breast:	n/a	n/a
40	PML	chr12:46660136-46664286	GM12878	blood:	n/a	chr12:46661270-46661278
41	CEBPB	chr12:46664042-46664365	HepG2	liver:	n/a	n/a
42	POLR2A	chr12:46660123-46664118	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr12:46660640-46664259	GM19193	blood:	n/a	n/a
44	POLR2A	chr12:46660034-46665824	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr12:46660660-46664310	GM19099	blood:	n/a	n/a
46	FOS	chr12:46663783-46664135	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:46664096-46664146	U87	brain:	n/a
2	chr12:46664096-46664146	GM12891	blood:	n/a
3	chr12:46664096-46664146	ProgFib	skin:	n/a
4	chr12:46664096-46664146	HIPEpiC	eye:	n/a
5	chr12:46664096-46664146	H1-hESC	embryonic stem cell:	embryo
6	chr12:46664096-46664146	ECC-1	luminal epithelium:	n/a
7	chr12:46664096-46664146	LNCaP	prostate:	n/a
8	chr12:46664096-46664146	NHDF-neo	bronchial:	n/a
9	chr12:46664096-46664146	MCF-7	breast:	n/a
10	chr12:46664096-46664146	Caco-2	colon:	n/a
11	chr12:46664096-46664146	T-47D	breast:	n/a
12	chr12:46664096-46664146	AG04449	skin:	fetal
13	chr12:46664096-46664146	NT2-D1	testis:	n/a
14	chr12:46664096-46664146	PrEC	prostate:	n/a
15	chr12:46664096-46664146	BJ	skin:	n/a
16	chr12:46664096-46664146	SKMC	muscle:	n/a
17	chr12:46664096-46664146	Hepatocyte	liver:	n/a
18	chr12:46664096-46664146	SK-N-SH_RA	brain:	n/a
19	chr12:46664096-46664146	GM12892	blood:	n/a
20	chr12:46664096-46664146	NHBE	bronchial:	n/a
21	chr12:46664096-46664146	HUVEC	blood vessel:	n/a
22	chr12:46664096-46664146	NH-A	brain:	n/a
23	chr12:46664096-46664146	SK-N-SH	brain:	n/a
24	chr12:46664096-46664146	A549	lung:	n/a
25	chr12:46664096-46664146	BE2_C	brain:	n/a
26	chr12:46664096-46664146	HEK293	kidney:	embryo
27	chr12:46664096-46664146	CMK	blood:	n/a
28	chr12:46664096-46664146	AG10803	skin:	n/a
29	chr12:46664096-46664146	GM12878	blood:	n/a
30	chr12:46664096-46664146	GM06990	blood:	n/a
31	chr12:46664096-46664146	HAEpiC	amniotic membrane:	n/a
32	chr12:46664096-46664146	HMEC	breast:	n/a
33	chr12:46664096-46664146	HRE	kidney:	n/a
34	chr12:46664096-46664146	HPAEpiC	pulmonary alveolar:	n/a
35	chr12:46664096-46664146	AG04450	lung:	fetal
36	chr12:46664096-46664146	AG09319	gingival:	n/a
37	chr12:46664096-46664146	Hela-S3	cervix:	n/a
38	chr12:46664096-46664146	HepG2	liver:	n/a
39	chr12:46664096-46664146	HEEpiC	esophagus:	n/a
40	chr12:46664096-46664146	Jurkat	blood:	n/a
41	chr12:46664096-46664146	ovcar-3	ovarian:	n/a
42	chr12:46664096-46664146	RPTEC	kidney:	n/a
43	chr12:46664096-46664146	HNPCEpiC	eye:	n/a
44	chr12:46664096-46664146	SAEC	small airway:	n/a
45	chr12:46664096-46664146	MCF10A-Er-Src	breast:	n/a
46	chr12:46664096-46664146	HCPEpiC	choroid plexus:	n/a
47	chr12:46664096-46664146	HRPEpiC	eye:	n/a
48	chr12:46664096-46664146	HRCEpiC	kidney:	n/a
49	chr12:46664096-46664146	PFSK-1	brain:	n/a
50	chr12:46664096-46664146	GM19239	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46661968..46664117-chr12:46775680..46778543,3	K562	blood:
2	chr12:46662773..46664298-chr12:46755324..46757349,2	MCF-7	breast:
3	chr12:46590494..46598595-chr12:46658954..46664180,10	MCF-7	breast:
4	chr1:11967303..11969441-chr12:46662756..46664296,2	MCF-7	breast:
5	chr12:46656458..46664971-chr12:46763618..46767965,19	MCF-7	breast:
6	chr12:46562964..46565138-chr12:46663936..46666612,3	MCF-7	breast:
7	chr12:46659532..46664131-chr12:46762494..46766775,7	K562	blood:
8	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
9	chr12:46660942..46665525-chr12:46775819..46780739,12	MCF-7	breast:
10	chr12:46383422..46386151-chr12:46661938..46664140,2	K562	blood:
11	chr12:46382717..46386243-chr12:46660668..46665434,7	MCF-7	breast:
12	chr12:46382760..46386151-chr12:46661620..46664692,5	K562	blood:
13	chr12:46663312..46666406-chr12:46754623..46758323,3	K562	blood:
14	chr12:46662257..46664463-chr12:48212247..48214266,2	MCF-7	breast:
15	chr12:46660616..46664726-chr12:46759249..46761419,3	MCF-7	breast:
16	chr12:46658047..46664131-chr12:46762494..46767686,10	K562	blood:

Variant related genes	Relation type
SLC38A1	TF binding region
SLC38A1	CpG island
ENSG00000061273	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000258096	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs7311450	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73280714	0.92[AFR][1000 genomes]
rs73280725	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73280732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73280735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73280763	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73280802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73282505	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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46658800-46664200	Active TSS	Placenta Amnion	Placenta Amnion
2	chr12:46659400-46664200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:46659400-46664200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:46659800-46664200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr12:46659800-46664200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:46659800-46664200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr12:46660000-46664200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr12:46660000-46664200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:46660200-46664200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:46660200-46664200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:46660400-46664200	Bivalent/Poised TSS	Fetal Kidney	kidney
12	chr12:46660600-46664200	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr12:46661000-46664200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:46662600-46664200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:46662600-46664200	Active TSS	Fetal Intestine Small	intestine
16	chr12:46662800-46664200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr12:46663000-46664400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr12:46663000-46664400	Flanking Active TSS	HMEC	breast
19	chr12:46663200-46664400	Active TSS	Fetal Brain Female	brain
20	chr12:46663200-46664400	Flanking Active TSS	NHEK	skin
21	chr12:46663400-46664200	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr12:46663400-46664200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:46663400-46664400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:46663600-46664200	Flanking Active TSS	Hela-S3	cervix
25	chr12:46663600-46664400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr12:46663600-46664400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr12:46663600-46664400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:46663600-46664600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr12:46663800-46664200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:46663800-46664200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr12:46663800-46664200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr12:46663800-46664200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:46663800-46664200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:46663800-46664200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:46663800-46664200	Enhancers	Fetal Brain Male	brain
36	chr12:46663800-46664200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:46663800-46664400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr12:46663800-46664400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:46663800-46664400	Active TSS	Brain Anterior Caudate	brain
40	chr12:46663800-46664600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:46663800-46664800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:46663800-46665200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:46664000-46664200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr12:46664000-46664200	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr12:46664000-46664200	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr12:46664000-46664200	Flanking Active TSS	Fetal Thymus	thymus
47	chr12:46664000-46664200	Active TSS	A549	lung
48	chr12:46664000-46664400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
49	chr12:46664000-46664400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr12:46664000-46664400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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