Variant report

Variant	rs3733311
Chromosome Location	chr4:22404455-22404456
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	chr4:22404446-22404539	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
GPR125	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13116724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13123910	0.81[ASN][1000 genomes]
rs13148867	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs16872606	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16872621	0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2045815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2047619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306135	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2323523	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs34062464	0.85[AMR][1000 genomes]
rs34537048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4697297	0.88[CHD][hapmap]
rs4697298	1.00[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs61791980	0.81[ASN][1000 genomes]
rs71608916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73800936	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817467	chr4:21602921-22422816	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv428756	chr4:22239826-22406106	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22368800-22418600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:22371600-22449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:22382600-22409600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:22383200-22438000	Weak transcription	Lung	lung
5	chr4:22383600-22442800	Weak transcription	A549	lung
6	chr4:22384200-22413000	Weak transcription	Fetal Heart	heart
7	chr4:22385400-22430400	Weak transcription	Psoas Muscle	Psoas
8	chr4:22386000-22446600	Weak transcription	Fetal Thymus	thymus
9	chr4:22388000-22411400	Weak transcription	NHDF-Ad	bronchial
10	chr4:22388000-22416600	Weak transcription	NHLF	lung
11	chr4:22388200-22432400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:22388200-22442800	Weak transcription	Brain Germinal Matrix	brain
13	chr4:22388400-22417800	Weak transcription	HUVEC	blood vessel
14	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
16	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
17	chr4:22390200-22404800	Weak transcription	Pancreas	Pancrea
18	chr4:22390200-22414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:22390600-22407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:22390600-22423600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr4:22390600-22439600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:22390600-22456200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:22390800-22407800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:22390800-22418000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:22390800-22420400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:22390800-22421400	Weak transcription	HepG2	liver
28	chr4:22390800-22429400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:22391400-22415400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:22393000-22435200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:22393400-22444800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:22393600-22407400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:22393600-22459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:22393800-22418000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:22393800-22446400	Weak transcription	NH-A	brain
36	chr4:22393800-22453000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:22394200-22405000	Weak transcription	Fetal Stomach	stomach
38	chr4:22397000-22428400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:22397200-22406200	Strong transcription	Fetal Intestine Large	intestine
40	chr4:22397200-22409000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:22397400-22408600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:22397800-22411600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:22397800-22412200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:22398400-22411800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:22398400-22423200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:22399000-22408000	Strong transcription	Fetal Lung	lung
47	chr4:22399000-22409000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:22399000-22416800	Strong transcription	Liver	Liver
49	chr4:22399400-22405000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:22399400-22405000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links