Variant report

Variant	rs60001273
Chromosome Location	chr2:30457020-30457021
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	SIN3AK20	chr2:30456891-30457666	MCF-7	breast:	n/a	n/a
2	SMC3	chr2:30456489-30457095	GM12878	blood:	n/a	n/a
3	REST	chr2:30456610-30457771	A549	lung:	n/a	n/a
4	MAX	chr2:30457003-30457233	GM12878	blood:	n/a	n/a
5	MXI1	chr2:30453058-30457443	SK-N-SH	brain:	n/a	n/a
6	BHLHE40	chr2:30456969-30457159	GM12878	blood:	n/a	n/a
7	FOSL2	chr2:30456174-30457941	A549	lung:	n/a	n/a
8	SIN3AK20	chr2:30456891-30457568	MCF-7	breast:	n/a	n/a
9	TCF12	chr2:30454035-30457915	A549	lung:	n/a	n/a
10	GATA3	chr2:30456899-30457892	MCF-7	breast:	n/a	chr2:30457705-30457715 chr2:30457813-30457822
11	REST	chr2:30456981-30457455	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr2:30456982-30457488	A549	lung:	n/a	n/a
13	POLR2A	chr2:30452975-30459369	IMR90	lung:	n/a	n/a
14	MAX	chr2:30456829-30457942	A549	lung:	n/a	n/a
15	EP300	chr2:30456661-30457231	GM12878	blood:	n/a	n/a
16	NFIC	chr2:30456899-30457399	GM12878	blood:	n/a	n/a
17	RAD21	chr2:30455319-30457535	IMR90	lung:	n/a	chr2:30457010-30457022
18	SIN3AK20	chr2:30456853-30457553	A549	lung:	n/a	n/a
19	HDAC2	chr2:30456987-30457516	MCF-7	breast:	n/a	n/a
20	MAX	chr2:30456932-30457566	MCF-7	breast:	n/a	n/a
21	MXI1	chr2:30456944-30457318	GM12878	blood:	n/a	n/a
22	MXI1	chr2:30453227-30457524	IMR90	lung:	n/a	n/a
23	NR2F2	chr2:30456907-30457654	MCF-7	breast:	n/a	n/a
24	POLR2A	chr2:30456927-30457166	A549	lung:	n/a	n/a
25	REST	chr2:30452536-30457549	H1-neurons	neurons:	n/a	chr2:30453631-30453649 chr2:30453642-30453655 chr2:30454097-30454110 chr2:30454675-30454688 chr2:30453921-30453934 chr2:30453992-30454005
26	MAX	chr2:30456829-30457599	A549	lung:	n/a	n/a
27	USF1	chr2:30456923-30457906	A549	lung:	n/a	n/a
28	JUND	chr2:30456954-30457608	A549	lung:	n/a	n/a
29	SIN3AK20	chr2:30456912-30457421	A549	lung:	n/a	n/a
30	HA-E2F1	chr2:30456893-30457559	MCF-7	breast:	n/a	n/a
31	POLR2A	chr2:30453153-30464183	SK-N-MC	brain:	n/a	n/a
32	CHD1	chr2:30453085-30459569	IMR90	lung:	n/a	chr2:30453328-30453338 chr2:30454803-30454813
33	EBF1	chr2:30456595-30457441	GM12878	blood:	n/a	chr2:30457084-30457095
34	REST	chr2:30456927-30457241	A549	lung:	n/a	n/a
35	SP1	chr2:30456781-30457651	A549	lung:	n/a	n/a
36	HDAC2	chr2:30456915-30457612	MCF-7	breast:	n/a	n/a
37	FOXA2	chr2:30457003-30457511	A549	lung:	n/a	n/a
38	BCL3	chr2:30456732-30457807	A549	lung:	n/a	n/a
39	EP300	chr2:30456303-30457569	A549	lung:	n/a	n/a
40	SIX5	chr2:30456747-30457501	A549	lung:	n/a	n/a
41	EP300	chr2:30456725-30457833	A549	lung:	n/a	chr2:30457703-30457717
42	POLR2A	chr2:30456968-30457379	A549	lung:	n/a	n/a
43	POLR2A	chr2:30456949-30457112	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr2:30453928-30457321	GM12878	blood:	n/a	n/a
45	ELF1	chr2:30456899-30457547	A549	lung:	n/a	n/a
46	RUNX3	chr2:30456908-30457829	GM12878	blood:	n/a	n/a
47	GATA3	chr2:30456721-30457742	A549	lung:	n/a	chr2:30457705-30457715
48	RCOR1	chr2:30456810-30459408	IMR90	lung:	n/a	n/a
49	NRF1	chr2:30456993-30457048	GM12878	blood:	n/a	n/a
50	REST	chr2:30456978-30457401	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
LBH	TF binding region

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs72787707	0.94[EUR][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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30453400-30457200	Active TSS	Ovary	ovary
2	chr2:30453400-30457200	Active TSS	Thymus	Thymus
3	chr2:30453400-30457400	Active TSS	Aorta	Aorta
4	chr2:30453800-30457400	Active TSS	NHDF-Ad	bronchial
5	chr2:30454400-30457200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:30455200-30463400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:30455600-30457200	Flanking Active TSS	Fetal Stomach	stomach
8	chr2:30455600-30457400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:30455600-30457400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:30455600-30457600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr2:30455600-30457800	Flanking Active TSS	GM12878-XiMat	blood
12	chr2:30455600-30458000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr2:30455600-30458200	Flanking Active TSS	Osteobl	bone
14	chr2:30455600-30460000	Transcr. at gene 5' and 3'	A549	lung
15	chr2:30455800-30457200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:30455800-30457200	Flanking Active TSS	Fetal Brain Female	brain
17	chr2:30455800-30457200	Flanking Active TSS	NH-A	brain
18	chr2:30455800-30457400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr2:30455800-30457400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:30455800-30457800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr2:30455800-30458000	Transcr. at gene 5' and 3'	Fetal Lung	lung
22	chr2:30455800-30458200	Transcr. at gene 5' and 3'	HSMM	muscle
23	chr2:30455800-30458400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
24	chr2:30456000-30457200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:30456000-30457200	Active TSS	Colonic Mucosa	Colon
26	chr2:30456000-30457200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
27	chr2:30456000-30457200	Enhancers	Spleen	Spleen
28	chr2:30456000-30457400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:30456000-30457400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:30456000-30457400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr2:30456000-30457600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
32	chr2:30456000-30457800	Enhancers	Pancreas	Pancrea
33	chr2:30456000-30458000	Bivalent Enhancer	Stomach Mucosa	stomach
34	chr2:30456000-30458400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:30456000-30458400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:30456000-30458400	Enhancers	HMEC	breast
37	chr2:30456000-30458600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
38	chr2:30456000-30464800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:30456200-30457200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
40	chr2:30456200-30457200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
41	chr2:30456200-30457200	Flanking Active TSS	Fetal Kidney	kidney
42	chr2:30456200-30457400	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr2:30456200-30457600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:30456200-30457600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:30456200-30457800	Enhancers	Gastric	stomach
46	chr2:30456200-30458200	Enhancers	Placenta	Placenta
47	chr2:30456400-30457200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
48	chr2:30456400-30457400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:30456400-30457400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:30456400-30458200	Flanking Active TSS	Duodenum Mucosa	Duodenum

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