Variant report

Variant	rs2239727
Chromosome Location	chr4:2822289-2822290
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	NFIC	chr4:2822148-2822714	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr4:2821988-2822675	ECC-1	luminal epithelium:	n/a	n/a
3	USF1	chr4:2822087-2822717	ECC-1	luminal epithelium:	n/a	n/a
4	MYC	chr4:2822221-2822578	MCF-7	breast:	n/a	chr4:2822314-2822323 chr4:2822313-2822323 chr4:2822314-2822324 chr4:2822313-2822324 chr4:2822315-2822322 chr4:2822314-2822323 chr4:2822312-2822325
5	POLR2A	chr4:2822016-2822645	MCF-7	breast:	n/a	n/a
6	MAX	chr4:2822171-2822631	MCF-7	breast:	n/a	chr4:2822314-2822323 chr4:2822313-2822323 chr4:2822314-2822324 chr4:2822313-2822324 chr4:2822315-2822322 chr4:2822314-2822323 chr4:2822312-2822325
7	MAX	chr4:2821945-2822780	ECC-1	luminal epithelium:	n/a	chr4:2822314-2822323 chr4:2822313-2822323 chr4:2822314-2822324 chr4:2822313-2822324 chr4:2822315-2822322 chr4:2822314-2822323 chr4:2822312-2822325
8	TCF12	chr4:2822169-2822766	ECC-1	luminal epithelium:	n/a	chr4:2822697-2822704 chr4:2822695-2822702 chr4:2822693-2822703
9	YY1	chr4:2822115-2822630	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr4:2822097-2822815	ECC-1	luminal epithelium:	n/a	chr4:2822697-2822704 chr4:2822695-2822702 chr4:2822693-2822703
11	POLR2A	chr4:2822028-2822539	ECC-1	luminal epithelium:	n/a	n/a
12	USF1	chr4:2822105-2822667	ECC-1	luminal epithelium:	n/a	n/a
13	YY1	chr4:2822081-2822638	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr4:2821986-2822748	ECC-1	luminal epithelium:	n/a	chr4:2822314-2822323 chr4:2822313-2822323 chr4:2822314-2822324 chr4:2822313-2822324 chr4:2822315-2822322 chr4:2822314-2822323 chr4:2822312-2822325

No.	Distal block	Cell Line	Cell type
1	chr4:2821818..2824046-chr4:2844267..2845999,2	MCF-7	breast:
2	chr4:2822103..2824509-chr4:2824545..2827389,5	MCF-7	breast:
3	chr4:2815555..2818329-chr4:2819380..2822501,3	MCF-7	breast:
4	chr4:2793845..2803067-chr4:2816443..2823671,22	MCF-7	breast:
5	chr4:2818848..2822289-chr4:2843327..2846796,5	MCF-7	breast:
6	chr4:2794084..2803742-chr4:2816227..2824357,23	MCF-7	breast:
7	chr4:2818590..2823604-chr4:2934968..2940177,8	MCF-7	breast:

Variant related genes	Relation type
SH3BP2	TF binding region
ENSG00000087274	Chromatin interaction
ENSG00000087266	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1623454	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1626813	0.89[ASN][1000 genomes]
rs1709003	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1794395	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs231399	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs231402	0.85[ASN][1000 genomes]
rs426192	0.83[ASN][1000 genomes]
rs430979	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62637887	0.87[ASN][1000 genomes]
rs9684650	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv470002	chr4:2701098-2836628	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878445	chr4:2704046-2831383	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878447	chr4:2723531-2831383	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv516797	chr4:2723531-2836628	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv878448	chr4:2723531-2846799	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
9	nsv878449	chr4:2744480-2831383	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv878452	chr4:2789184-2830076	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv461162	chr4:2794320-2846799	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv593436	chr4:2794320-2846799	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2815800-2827000	Weak transcription	Fetal Heart	heart
2	chr4:2820000-2825000	Weak transcription	Brain Substantia Nigra	brain
3	chr4:2820400-2823200	Genic enhancers	Spleen	Spleen
4	chr4:2820400-2824200	Strong transcription	Liver	Liver
5	chr4:2820400-2827600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:2820600-2822400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:2820600-2822400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr4:2820600-2822400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:2820600-2822400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:2820600-2823200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:2820600-2824200	Weak transcription	Left Ventricle	heart
12	chr4:2820600-2825400	Weak transcription	Osteobl	bone
13	chr4:2820600-2825600	Weak transcription	Brain Anterior Caudate	brain
14	chr4:2820600-2825800	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:2820600-2827200	Weak transcription	Aorta	Aorta
16	chr4:2820600-2827200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:2820600-2832400	Weak transcription	NHDF-Ad	bronchial
18	chr4:2820600-2839000	Weak transcription	Right Atrium	heart
19	chr4:2820600-2839200	Weak transcription	Brain Angular Gyrus	brain
20	chr4:2820600-2844600	Weak transcription	Psoas Muscle	Psoas
21	chr4:2820800-2822400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:2820800-2822400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:2820800-2822600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:2820800-2822600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:2820800-2822600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:2820800-2822600	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr4:2820800-2822600	Weak transcription	Ovary	ovary
28	chr4:2820800-2822800	Genic enhancers	Placenta	Placenta
29	chr4:2820800-2823800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:2820800-2824200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:2820800-2824400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:2820800-2824600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:2820800-2824600	Weak transcription	NHLF	lung
34	chr4:2820800-2826200	Weak transcription	HSMM	muscle
35	chr4:2820800-2827000	Weak transcription	Fetal Kidney	kidney
36	chr4:2820800-2828200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:2820800-2835200	Weak transcription	HUVEC	blood vessel
38	chr4:2820800-2835400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr4:2820800-2839600	Weak transcription	NHEK	skin
40	chr4:2821000-2822400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr4:2821000-2822400	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr4:2821000-2822400	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:2821000-2822400	Weak transcription	HSMMtube	muscle
44	chr4:2821000-2822600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:2821000-2823000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:2821000-2823200	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr4:2821000-2824400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr4:2821000-2824600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr4:2821000-2824800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr4:2821000-2825000	Weak transcription	Colon Smooth Muscle	Colon

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