Variant report

Variant	rs2972087
Chromosome Location	chr2:55335045-55335046
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	SP1	chr2:55334345-55335050	A549	lung:	n/a	n/a
2	SIN3AK20	chr2:55334517-55335296	MCF-7	breast:	n/a	n/a
3	TCF12	chr2:55334304-55335246	A549	lung:	n/a	n/a
4	FOSL2	chr2:55334476-55335081	A549	lung:	n/a	chr2:55334573-55334584
5	EP300	chr2:55334354-55335076	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr2:55333859-55335147	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr2:55334426-55335103	MCF-7	breast:	n/a	chr2:55334450-55334459
8	SP1	chr2:55334361-55335119	A549	lung:	n/a	n/a
9	NR2F2	chr2:55334586-55335198	MCF-7	breast:	n/a	n/a
10	GATA2	chr2:55334656-55335094	SH-SY5Y	brain:	n/a	n/a
11	GATA3	chr2:55334378-55335152	SK-N-SH	brain:	n/a	chr2:55334450-55334459
12	SIN3AK20	chr2:55334544-55335223	MCF-7	breast:	n/a	n/a
13	TEAD4	chr2:55334595-55335073	MCF-7	breast:	n/a	n/a
14	GATA3	chr2:55334498-55335185	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr2:55334553-55335236	MCF-7	breast:	n/a	n/a
16	HDAC2	chr2:55334632-55335124	MCF-7	breast:	n/a	chr2:55335052-55335060
17	NR2F2	chr2:55334463-55335155	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55275100..55278867-chr2:55332257..55335062,4	K562	blood:
2	chr2:55332689..55335529-chr2:55338275..55340328,2	MCF-7	breast:
3	chr2:55331372..55335609-chr2:55337059..55340698,6	K562	blood:

Variant related genes	Relation type
ENSG00000266376	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10183953	0.82[JPT][hapmap]
rs10439479	0.82[JPT][hapmap]
rs11694920	0.82[JPT][hapmap]
rs12464094	1.00[AFR][1000 genomes]
rs13002841	1.00[JPT][hapmap]
rs1437389	0.82[JPT][hapmap]
rs1437392	0.82[JPT][hapmap]
rs1561231	0.82[JPT][hapmap]
rs2043714	0.82[JPT][hapmap]
rs2118283	0.82[JPT][hapmap]
rs2589081	0.82[JPT][hapmap]
rs2589082	0.82[JPT][hapmap]
rs2920843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2920845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2920846	1.00[ASN][1000 genomes]
rs2920872	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2968807	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2968810	0.83[EUR][1000 genomes]
rs2968812	0.87[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2968813	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2968814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2968816	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972084	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2972085	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972086	0.95[ASN][1000 genomes]
rs2972091	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4233959	0.82[JPT][hapmap]
rs4591380	0.82[JPT][hapmap]
rs6545476	0.82[JPT][hapmap]
rs6545479	0.82[JPT][hapmap]
rs6713058	0.82[JPT][hapmap]
rs6715694	0.82[JPT][hapmap]
rs6716066	0.82[JPT][hapmap]
rs6719579	0.82[JPT][hapmap]
rs6723870	0.82[JPT][hapmap]
rs6747682	0.82[JPT][hapmap]
rs6750501	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006172	chr2:55322883-55340812	Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3345871	chr2:55323717-55336931	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3457756	chr2:55323755-55336917	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3457755	chr2:55323788-55336864	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3457757	chr2:55323788-55336864	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv9883	chr2:55323841-55336774	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv999212	chr2:55324276-55340812	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2421886	chr2:55324288-55335045	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3693301	chr2:55324960-55335045	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv517331	chr2:55324960-55335045	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv817951	chr2:55324960-55335045	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55321600-55339400	Weak transcription	Thymus	Thymus
2	chr2:55321800-55336400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:55325200-55340400	Weak transcription	Gastric	stomach
4	chr2:55327800-55335400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:55327800-55338600	Weak transcription	Lung	lung
6	chr2:55327800-55338600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:55329000-55338600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:55329600-55342600	Weak transcription	NHEK	skin
9	chr2:55329800-55336600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:55330600-55336000	Weak transcription	Adipose Nuclei	Adipose
11	chr2:55330600-55338600	Weak transcription	Aorta	Aorta
12	chr2:55330800-55336000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:55331200-55339000	Weak transcription	Dnd41	blood
14	chr2:55331800-55338600	Weak transcription	Fetal Thymus	thymus
15	chr2:55332000-55343400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:55332400-55338400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr2:55332400-55338400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:55332600-55337200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:55332800-55336600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:55332800-55337800	Enhancers	NHLF	lung
21	chr2:55332800-55338000	Enhancers	Hela-S3	cervix
22	chr2:55332800-55338400	Enhancers	HSMM	muscle
23	chr2:55332800-55338600	Enhancers	Osteobl	bone
24	chr2:55333000-55335800	Enhancers	NH-A	brain
25	chr2:55333000-55336400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:55333000-55338600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:55333200-55337200	Enhancers	Fetal Heart	heart
28	chr2:55333200-55338600	Enhancers	NHDF-Ad	bronchial
29	chr2:55333200-55338800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:55333600-55335600	Weak transcription	Fetal Intestine Large	intestine
31	chr2:55333600-55336200	Weak transcription	K562	blood
32	chr2:55333600-55338600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:55334000-55337000	Enhancers	Colon Smooth Muscle	Colon
34	chr2:55334000-55337000	Enhancers	Rectal Smooth Muscle	rectum
35	chr2:55334000-55337400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:55334000-55338600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:55334000-55338600	Enhancers	Brain Hippocampus Middle	brain
38	chr2:55334200-55335800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:55334200-55336400	Enhancers	Brain Substantia Nigra	brain
40	chr2:55334200-55337000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:55334200-55338600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:55334400-55337600	Enhancers	Stomach Smooth Muscle	stomach
43	chr2:55334400-55340800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:55334600-55335200	Enhancers	Stomach Mucosa	stomach
45	chr2:55334600-55335200	Flanking Active TSS	A549	lung
46	chr2:55334600-55336200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:55334600-55338400	Enhancers	HepG2	liver
48	chr2:55334800-55335200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:55334800-55335200	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:55334800-55335200	Flanking Active TSS	HSMMtube	muscle

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