Variant report

Variant	rs3732356
Chromosome Location	chr3:119529113-119529114
allele	G/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	PAX5	chr3:119529029-119529306	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:119528801-119529218	H1-hESC	embryonic stem cell:	n/a	n/a
4	GABPA	chr3:119528852-119529178	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:119528623-119529341	GM19099	blood:	n/a	n/a
6	CTCF	chr3:119529080-119529230	HFF	foreskin:	n/a	n/a
7	CTCF	chr3:119529054-119529334	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:119528613-119529429	GM19193	blood:	n/a	n/a
9	CTCF	chr3:119529021-119529356	GM12892	blood:	n/a	n/a
10	POLR2A	chr3:119528645-119529429	GM18526	blood:	n/a	n/a
11	REST	chr3:119528702-119529428	HL-60	blood:	n/a	chr3:119528822-119528835
12	RUNX3	chr3:119528430-119529541	GM12878	blood:	n/a	n/a
13	CTCF	chr3:119529060-119529210	HRPEpiC	eye:	n/a	n/a
14	PAX5	chr3:119528925-119529399	GM12878	blood:	n/a	n/a
15	YY1	chr3:119528830-119529337	GM12891	blood:	n/a	chr3:119528854-119528868
16	POLR2A	chr3:119528911-119529331	GM12891	blood:	n/a	n/a
17	CTCF	chr3:119529100-119529250	HFF-Myc	foreskin:	n/a	n/a
18	CTCF	chr3:119529076-119529243	IMR90	lung:	n/a	n/a
19	POLR2A	chr3:119528918-119529218	HUVEC	blood vessel:	n/a	n/a
20	YY1	chr3:119528709-119529308	GM12892	blood:	n/a	chr3:119528816-119528827 chr3:119528854-119528868
21	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
22	POLR2A	chr3:119529101-119529217	ProgFib	skin:	n/a	n/a
23	ELF1	chr3:119528697-119529378	MCF-7	breast:	n/a	n/a
24	EBF1	chr3:119528588-119529316	GM12878	blood:	n/a	chr3:119528730-119528740
25	POLR2A	chr3:119528786-119529269	H1-hESC	embryonic stem cell:	n/a	n/a
26	ELF1	chr3:119528415-119529361	GM12878	blood:	n/a	n/a
27	CTCF	chr3:119529100-119529250	GM12871	blood:	n/a	n/a
28	NRF1	chr3:119528975-119529323	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD2	chr3:119528587-119529361	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:119528724-119529380	GM15510	blood:	n/a	n/a
31	CTCF	chr3:119529048-119529323	MCF-7	breast:	n/a	n/a
32	POLR2A	chr3:119528906-119529262	GM12891	blood:	n/a	n/a
33	CTCF	chr3:119529042-119529322	MCF-7	breast:	n/a	n/a
34	STAT5A	chr3:119528416-119529234	GM12878	blood:	n/a	chr3:119528755-119528763 chr3:119528822-119528834
35	MYC	chr3:119528941-119529304	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:119528469-119529445	GM12891	blood:	n/a	n/a
37	BHLHE40	chr3:119528452-119529393	GM12878	blood:	n/a	n/a
38	CTCF	chr3:119529017-119529339	GM19239	blood:	n/a	n/a
39	CTCF	chr3:119529080-119529308	GM13977	blood:	n/a	n/a
40	SMC3	chr3:119529017-119529429	GM12878	blood:	n/a	n/a
41	TCF3	chr3:119528876-119529323	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:119528742-119529433	GM12892	blood:	n/a	n/a
43	HA-E2F1	chr3:119528744-119529335	MCF-7	breast:	n/a	n/a
44	POLR2A	chr3:119528940-119529249	MCF-7	breast:	n/a	n/a
45	ZNF143	chr3:119529002-119529381	GM12878	blood:	n/a	n/a
46	CTCF	chr3:119529080-119529230	GM12868	blood:	n/a	n/a
47	ELF1	chr3:119528402-119529352	GM12878	blood:	n/a	n/a
48	MAX	chr3:119528797-119529427	MCF-7	breast:	n/a	n/a
49	CTCF	chr3:119529100-119529250	AG09319	gingival:	n/a	n/a
50	CTCF	chr3:119529002-119529343	GM12891	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]
rs1464600	0.95[ASN][1000 genomes]
rs1464601	0.97[ASN][1000 genomes]
rs2461816	0.97[ASN][1000 genomes]
rs2461824	0.95[ASN][1000 genomes]
rs2472680	0.97[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	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	chr3:119528200-119529200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:119528200-119529400	Active TSS	HSMM	muscle
5	chr3:119528200-119529600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:119528200-119533800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:119528400-119529200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr3:119528400-119529200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr3:119528400-119529400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:119528400-119529400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:119528400-119529400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr3:119528400-119529400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr3:119528400-119529400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:119528400-119529400	Active TSS	Fetal Kidney	kidney
15	chr3:119528400-119529400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
16	chr3:119528400-119529600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr3:119528400-119529600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr3:119528400-119529600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:119528400-119529600	Active TSS	Rectal Smooth Muscle	rectum
20	chr3:119528600-119529200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:119528600-119529200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:119528600-119529200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr3:119528600-119529200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:119528600-119529200	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr3:119528600-119529200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:119528600-119529200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr3:119528600-119529200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:119528600-119529200	Active TSS	Brain Substantia Nigra	brain
29	chr3:119528600-119529200	Flanking Active TSS	Placenta	Placenta
30	chr3:119528600-119529200	Active TSS	Ovary	ovary
31	chr3:119528600-119529200	Active TSS	Right Atrium	heart
32	chr3:119528600-119529400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:119528600-119529400	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr3:119528600-119529400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:119528600-119529400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:119528600-119529400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:119528600-119529400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr3:119528600-119529400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr3:119528600-119529400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:119528600-119529400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:119528600-119529400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:119528600-119529400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:119528600-119529400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr3:119528600-119529400	Active TSS	Aorta	Aorta
45	chr3:119528600-119529400	Active TSS	Brain Anterior Caudate	brain
46	chr3:119528600-119529400	Flanking Active TSS	Colonic Mucosa	Colon
47	chr3:119528600-119529400	Active TSS	Colon Smooth Muscle	Colon
48	chr3:119528600-119529400	Flanking Active TSS	Esophagus	oesophagus
49	chr3:119528600-119529400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
50	chr3:119528600-119529400	Enhancers	Fetal Brain Male	brain

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