Variant report

Variant	rs12721616
Chromosome Location	chr3:119528879-119528880
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	chr3:119528777-119529327	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:119528801-119529218	H1-hESC	embryonic stem cell:	n/a	n/a
3	GABPA	chr3:119528852-119529178	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:119528623-119529341	GM19099	blood:	n/a	n/a
5	POLR2A	chr3:119528613-119529429	GM19193	blood:	n/a	n/a
6	POLR2A	chr3:119528645-119529429	GM18526	blood:	n/a	n/a
7	REST	chr3:119528702-119529428	HL-60	blood:	n/a	chr3:119528822-119528835
8	RUNX3	chr3:119528430-119529541	GM12878	blood:	n/a	n/a
9	YY1	chr3:119528830-119529337	GM12891	blood:	n/a	chr3:119528854-119528868
10	YY1	chr3:119528709-119529308	GM12892	blood:	n/a	chr3:119528816-119528827 chr3:119528854-119528868
11	MAX	chr3:119528401-119529420	H1-hESC	embryonic stem cell:	n/a	chr3:119528651-119528662 chr3:119528652-119528662 chr3:119528647-119528666 chr3:119528517-119528526 chr3:119528651-119528662 chr3:119528650-119528663
12	ELF1	chr3:119528697-119529378	MCF-7	breast:	n/a	n/a
13	EBF1	chr3:119528588-119529316	GM12878	blood:	n/a	chr3:119528730-119528740
14	POLR2A	chr3:119528786-119529269	H1-hESC	embryonic stem cell:	n/a	n/a
15	ELF1	chr3:119528415-119529361	GM12878	blood:	n/a	n/a
16	CHD2	chr3:119528587-119529361	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:119528724-119529380	GM15510	blood:	n/a	n/a
18	STAT5A	chr3:119528416-119529234	GM12878	blood:	n/a	chr3:119528755-119528763 chr3:119528822-119528834
19	POLR2A	chr3:119528469-119529445	GM12891	blood:	n/a	n/a
20	BHLHE40	chr3:119528452-119529393	GM12878	blood:	n/a	n/a
21	TCF3	chr3:119528876-119529323	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:119528742-119529433	GM12892	blood:	n/a	n/a
23	HA-E2F1	chr3:119528744-119529335	MCF-7	breast:	n/a	n/a
24	MAZ	chr3:119528601-119528947	GM12878	blood:	n/a	chr3:119528651-119528662 chr3:119528652-119528662 chr3:119528647-119528666 chr3:119528651-119528662 chr3:119528650-119528663
25	ELF1	chr3:119528402-119529352	GM12878	blood:	n/a	n/a
26	MAX	chr3:119528797-119529427	MCF-7	breast:	n/a	n/a
27	POLR2A	chr3:119528716-119529306	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:119528594-119529388	GM18951	blood:	n/a	n/a
29	E2F6	chr3:119528438-119529541	H1-hESC	embryonic stem cell:	n/a	n/a
30	SPI1	chr3:119528434-119529053	GM12878	blood:	n/a	chr3:119528600-119528613 chr3:119528603-119528610
31	E2F6	chr3:119528447-119529331	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:119528829-119529341	HL-60	blood:	n/a	n/a
33	TBP	chr3:119528613-119529321	H1-hESC	embryonic stem cell:	n/a	n/a
34	EBF1	chr3:119528589-119529297	GM12878	blood:	n/a	chr3:119528730-119528740
35	SRF	chr3:119528489-119528881	GM12878	blood:	n/a	chr3:119528857-119528867
36	MAX	chr3:119528470-119529325	H1-hESC	embryonic stem cell:	n/a	chr3:119528651-119528662 chr3:119528652-119528662 chr3:119528647-119528666 chr3:119528517-119528526 chr3:119528651-119528662 chr3:119528650-119528663
37	MAX	chr3:119528394-119529465	H1-hESC	embryonic stem cell:	n/a	chr3:119528651-119528662 chr3:119528652-119528662 chr3:119528647-119528666 chr3:119528517-119528526 chr3:119528651-119528662 chr3:119528650-119528663
38	POLR2A	chr3:119528619-119529411	GM12892	blood:	n/a	n/a
39	POLR2A	chr3:119528576-119529393	GM18505	blood:	n/a	n/a
40	RELA	chr3:119528552-119529418	GM18951	blood:	n/a	n/a
41	MXI1	chr3:119528531-119529281	H1-hESC	embryonic stem cell:	n/a	n/a
42	HMGN3	chr3:119528871-119529171	K562	blood:	n/a	n/a
43	POLR2A	chr3:119528568-119529331	GM12878	blood:	n/a	n/a
44	ELF1	chr3:119528686-119529373	MCF-7	breast:	n/a	n/a
45	CTCF	chr3:119528840-119528990	GM12870	blood:	n/a	n/a
46	POLR2A	chr3:119528448-119529416	HL-60	blood:	n/a	n/a
47	POLR2A	chr3:119528851-119529370	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:119528801-119529378	MCF-7	breast:	n/a	n/a
49	YY1	chr3:119528861-119529367	GM12878	blood:	n/a	n/a
50	ELK1	chr3:119528496-119529127	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119421341..119422260-chr3:119528762..119529781,3	MCF-7	breast:
2	chr3:119527283..119529245-chr3:119900596..119902132,2	MCF-7	breast:

Variant related genes	Relation type
NR1I2	TF binding region
ENSG00000183833	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12721611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16830442	1.00[AMR][1000 genomes]
rs72963177	1.00[AMR][1000 genomes]
rs72963183	1.00[AMR][1000 genomes]
rs72963185	1.00[AMR][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	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119516800-119534600	Weak transcription	HepG2	liver
2	chr3:119525000-119532400	Weak transcription	Small Intestine	intestine
3	chr3:119525200-119529000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:119528000-119529000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:119528200-119529200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:119528200-119529400	Active TSS	HSMM	muscle
7	chr3:119528200-119529600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:119528200-119533800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:119528400-119529200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr3:119528400-119529200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr3:119528400-119529400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:119528400-119529400	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:119528400-119529400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr3:119528400-119529400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr3:119528400-119529400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:119528400-119529400	Active TSS	Fetal Kidney	kidney
17	chr3:119528400-119529400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
18	chr3:119528400-119529600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr3:119528400-119529600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr3:119528400-119529600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:119528400-119529600	Active TSS	Rectal Smooth Muscle	rectum
22	chr3:119528600-119529000	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:119528600-119529000	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr3:119528600-119529000	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr3:119528600-119529000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:119528600-119529000	Active TSS	Duodenum Mucosa	Duodenum
27	chr3:119528600-119529000	Flanking Active TSS	Fetal Brain Female	brain
28	chr3:119528600-119529000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr3:119528600-119529000	Active TSS	Left Ventricle	heart
30	chr3:119528600-119529000	Flanking Active TSS	Thymus	Thymus
31	chr3:119528600-119529200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:119528600-119529200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:119528600-119529200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr3:119528600-119529200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:119528600-119529200	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr3:119528600-119529200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:119528600-119529200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr3:119528600-119529200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:119528600-119529200	Active TSS	Brain Substantia Nigra	brain
40	chr3:119528600-119529200	Flanking Active TSS	Placenta	Placenta
41	chr3:119528600-119529200	Active TSS	Ovary	ovary
42	chr3:119528600-119529200	Active TSS	Right Atrium	heart
43	chr3:119528600-119529400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:119528600-119529400	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr3:119528600-119529400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:119528600-119529400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:119528600-119529400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:119528600-119529400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:119528600-119529400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr3:119528600-119529400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin

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