Variant report

Variant	rs3806572
Chromosome Location	chr2:55238677-55238678
allele	C/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	POLR2A	chr2:55222320-55241658	K562	blood:	n/a	n/a
2	POLR2A	chr2:55238388-55238695	SK-N-SH	brain:	n/a	n/a
3	TEAD4	chr2:55238608-55239335	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55238547..55240641-chr2:55252176..55254092,2	MCF-7	breast:
2	chr2:55236989..55239116-chr2:55240470..55242602,2	K562	blood:
3	chr2:55224190..55226193-chr2:55238312..55240025,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10084445	1.00[YRI][hapmap]
rs10170102	0.83[AFR][1000 genomes]
rs10173203	0.90[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10181115	0.83[AFR][1000 genomes]
rs10189094	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10191684	0.84[AFR][1000 genomes]
rs11125554	1.00[YRI][hapmap]
rs13394823	0.81[AFR][1000 genomes]
rs13394824	0.81[AFR][1000 genomes]
rs17046567	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs17046569	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3198123	0.95[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6705519	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6757907	0.84[CEU][hapmap]
rs7601895	0.84[CEU][hapmap]

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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55227600-55239000	Weak transcription	Hela-S3	cervix
3	chr2:55232200-55244800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:55233200-55240400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:55235600-55240600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:55236200-55239600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr2:55236400-55238800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr2:55236600-55241400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr2:55236800-55240800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:55236800-55243400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr2:55237000-55243600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr2:55237200-55239600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr2:55237200-55241600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:55237400-55239400	Enhancers	Primary B cells from peripheral blood	blood
17	chr2:55237400-55240800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr2:55237400-55242800	Enhancers	HSMMtube	muscle
19	chr2:55237600-55238800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:55237600-55239000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:55237600-55239000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:55237600-55239000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:55237600-55239000	Enhancers	Aorta	Aorta
24	chr2:55237600-55239000	Enhancers	Brain Anterior Caudate	brain
25	chr2:55237600-55239200	Enhancers	Fetal Muscle Leg	muscle
26	chr2:55237600-55239400	Enhancers	HSMM	muscle
27	chr2:55237600-55239600	Enhancers	NHEK	skin
28	chr2:55237600-55239800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:55237600-55239800	Weak transcription	Brain Angular Gyrus	brain
30	chr2:55237600-55240000	Enhancers	Dnd41	blood
31	chr2:55237600-55240400	Weak transcription	Fetal Brain Male	brain
32	chr2:55237600-55240800	Enhancers	Colon Smooth Muscle	Colon
33	chr2:55237600-55241000	Enhancers	NH-A	brain
34	chr2:55237600-55241200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:55237600-55241400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr2:55237600-55241400	Enhancers	Fetal Lung	lung
37	chr2:55237600-55241600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:55237600-55242000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr2:55237600-55243600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:55237600-55246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
42	chr2:55237600-55249600	Weak transcription	Gastric	stomach
43	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:55237600-55258600	Weak transcription	Ovary	ovary
45	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
46	chr2:55237800-55239000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:55237800-55239000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr2:55237800-55239000	Weak transcription	Colonic Mucosa	Colon
49	chr2:55237800-55239000	Enhancers	Fetal Intestine Large	intestine
50	chr2:55237800-55239200	Enhancers	Primary B cells from cord blood	blood

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