Variant report

Variant	rs771253
Chromosome Location	chr2:7114174-7114175
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	STAT3	chr2:7114087-7114406	MCF10A-Er-Src	breast:	n/a	n/a
2	FOSL1	chr2:7113853-7114567	HCT-116	colon:	n/a	n/a
3	POLR2A	chr2:7114032-7114384	HCT-116	colon:	n/a	n/a
4	STAT3	chr2:7114095-7114625	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr2:7114157-7114329	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr2:7114042-7114351	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr2:7114048-7114430	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr2:7114017-7114421	MCF10A-Er-Src	breast:	n/a	n/a
9	MAX	chr2:7113739-7114598	HCT-116	colon:	n/a	n/a
10	STAT3	chr2:7114003-7114409	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr2:7114005-7114524	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr2:7114005-7114479	MCF10A-Er-Src	breast:	n/a	n/a
13	EP300	chr2:7113893-7114634	ECC-1	luminal epithelium:	n/a	n/a
14	TEAD4	chr2:7114071-7114529	ECC-1	luminal epithelium:	n/a	n/a
15	JUND	chr2:7113952-7114614	HCT-116	colon:	n/a	n/a
16	SP1	chr2:7113807-7114606	HCT-116	colon:	n/a	n/a
17	JUND	chr2:7113825-7114567	HCT-116	colon:	n/a	n/a
18	SP1	chr2:7113779-7114621	HCT-116	colon:	n/a	n/a
19	FOS	chr2:7114046-7114408	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:7057303..7059038-chr2:7114165..7115903,2	K562	blood:
2	chr2:7113332..7116286-chr2:9136805..9139495,2	MCF-7	breast:
3	chr2:7065097..7066741-chr2:7112184..7114861,2	K562	blood:

Variant related genes	Relation type
RNF144A	TF binding region
ENSG00000228203	Chromatin interaction
ENSG00000151692	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10495548	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs10495549	0.86[MEX][hapmap]
rs13393491	1.00[JPT][hapmap]
rs13399190	1.00[JPT][hapmap]
rs13408347	0.89[ASN][1000 genomes]
rs1797554	0.81[ASN][1000 genomes]
rs2292931	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs6741819	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs700943	0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[ASN][1000 genomes]
rs771256	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs771257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs771259	1.00[JPT][hapmap]
rs771263	1.00[JPT][hapmap]
rs771265	1.00[JPT][hapmap]
rs771266	0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[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	nsv833326	chr2:6985027-7142564	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv2598	chr2:7088737-7133415	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs771253	RNF144A	cis	cerebellum	SCAN
rs771253	ODC1	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7083800-7129600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:7084200-7122200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:7085000-7120200	Weak transcription	Fetal Intestine Small	intestine
4	chr2:7096800-7120600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:7097200-7126200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:7098000-7115800	Weak transcription	HepG2	liver
7	chr2:7099000-7123600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:7101000-7117400	Weak transcription	Right Atrium	heart
9	chr2:7101000-7130000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:7101200-7116000	Weak transcription	Gastric	stomach
11	chr2:7101200-7117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:7101200-7126200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:7101200-7144000	Weak transcription	Aorta	Aorta
14	chr2:7101200-7154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:7101400-7117200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:7101600-7117200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:7101800-7126200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:7102000-7117400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:7102200-7117400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:7102400-7117000	Weak transcription	Fetal Brain Male	brain
21	chr2:7104200-7120600	Strong transcription	Dnd41	blood
22	chr2:7105600-7120600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:7106200-7123200	Strong transcription	Primary T cells from cord blood	blood
24	chr2:7107200-7117000	Weak transcription	Fetal Lung	lung
25	chr2:7108800-7115400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:7109000-7114600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:7109200-7115800	Weak transcription	Left Ventricle	heart
28	chr2:7109200-7116000	Weak transcription	Fetal Heart	heart
29	chr2:7109200-7117400	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:7109200-7137000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:7109400-7117400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:7109800-7116000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:7110400-7114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:7110600-7120200	Weak transcription	Fetal Thymus	thymus
35	chr2:7110800-7115000	Enhancers	Brain Substantia Nigra	brain
36	chr2:7111000-7115400	Weak transcription	Esophagus	oesophagus
37	chr2:7111000-7118000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:7111200-7117000	Weak transcription	Brain Germinal Matrix	brain
39	chr2:7111200-7117200	Weak transcription	Fetal Brain Female	brain
40	chr2:7111600-7126400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr2:7111800-7116000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:7111800-7117400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:7111800-7118000	Weak transcription	Right Ventricle	heart
44	chr2:7112000-7116200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:7112000-7118200	Weak transcription	Spleen	Spleen
46	chr2:7112200-7117400	Weak transcription	Adipose Nuclei	Adipose
47	chr2:7112400-7114600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:7112400-7117200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:7112400-7117400	Weak transcription	Psoas Muscle	Psoas
50	chr2:7112400-7117400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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