Variant report

Variant	rs2289911
Chromosome Location	chr2:233704252-233704253
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	MYC	chr2:233704161-233704837	NB4	blood:	n/a	n/a
2	POLR2A	chr2:233704007-233704259	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:233704237-233704886	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
GIGYF2	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1078323	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10933406	0.93[CEU][hapmap]
rs1104764	0.89[CEU][hapmap]
rs11688166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11689851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12105766	0.92[CEU][hapmap]
rs12619195	0.93[CEU][hapmap]
rs12993791	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13001052	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13007579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13008436	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13009957	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13021823	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13024330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1446309	1.00[CHB][hapmap]
rs17164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1973675	0.92[CEU][hapmap]
rs2344613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2592104	0.80[EUR][1000 genomes]
rs2675972	0.83[EUR][1000 genomes]
rs283465	0.84[EUR][1000 genomes]
rs283467	0.83[EUR][1000 genomes]
rs283470	0.93[CEU][hapmap]
rs283487	0.83[EUR][1000 genomes]
rs34707169	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35491427	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4973563	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4973564	0.88[CEU][hapmap]
rs4973569	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6704763	0.92[CEU][hapmap]
rs6717048	0.93[CEU][hapmap]
rs6733495	0.93[CEU][hapmap]
rs737027	0.92[CEU][hapmap]
rs7560115	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs778371	0.90[ASN][1000 genomes]
rs921055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs974321	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460134	chr2:233639909-233714686	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv584696	chr2:233639909-233714686	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:233667600-233726400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233689000-233713000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:233689200-233726400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:233691200-233717200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:233695400-233705600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:233696400-233714200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:233698400-233723600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:233699200-233704600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:233699200-233712000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:233699200-233717000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:233699800-233717000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:233700000-233704600	Strong transcription	Fetal Stomach	stomach
14	chr2:233700000-233705200	Weak transcription	Fetal Brain Male	brain
15	chr2:233700200-233704600	Genic enhancers	Duodenum Mucosa	Duodenum
16	chr2:233700600-233708800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:233700600-233714200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:233700800-233707200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:233701000-233707400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:233701000-233729200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:233701400-233705400	Strong transcription	Brain Germinal Matrix	brain
22	chr2:233701600-233704600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:233701600-233704600	Genic enhancers	Rectal Mucosa Donor 29	rectum
24	chr2:233701600-233704600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
25	chr2:233701800-233707400	Weak transcription	Right Atrium	heart
26	chr2:233701800-233717000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:233702000-233704400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:233702000-233704400	Weak transcription	Ovary	ovary
29	chr2:233702000-233704400	Weak transcription	HSMMtube	muscle
30	chr2:233702000-233704600	Enhancers	Primary hematopoietic stem cells	blood
31	chr2:233702000-233704600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:233702000-233706400	Weak transcription	Left Ventricle	heart
33	chr2:233702000-233706800	Weak transcription	Esophagus	oesophagus
34	chr2:233702000-233706800	Weak transcription	Lung	lung
35	chr2:233702200-233704400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:233702200-233704800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:233702200-233704800	Enhancers	Hela-S3	cervix
38	chr2:233702400-233704400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:233702400-233704600	Genic enhancers	NHEK	skin
40	chr2:233702400-233704800	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr2:233702400-233704800	Enhancers	HUVEC	blood vessel
42	chr2:233702400-233705200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr2:233702400-233705400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr2:233702600-233704400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr2:233702600-233704400	Enhancers	Brain Substantia Nigra	brain
46	chr2:233702600-233704400	Enhancers	K562	blood
47	chr2:233702600-233704600	Genic enhancers	Primary T cells from cord blood	blood
48	chr2:233702600-233704600	Enhancers	Small Intestine	intestine
49	chr2:233702600-233708800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:233702800-233704600	Genic enhancers	Adipose Nuclei	Adipose

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