Variant report

Variant	rs6544223
Chromosome Location	chr2:39609538-39609539
allele	A/C
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	GATA3	chr2:39609019-39609715	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39592431..39595037-chr2:39606994..39609633,2	MCF-7	breast:
2	chr2:39594087..39595987-chr2:39607916..39609547,2	MCF-7	breast:
3	chr2:39608927..39611189-chr2:39667171..39668738,2	K562	blood:
4	chr2:39608115..39611189-chr2:39665899..39668671,3	K562	blood:
5	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:

Variant related genes	Relation type
MAP4K3	TF binding region
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10169391	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10170424	0.89[AFR][1000 genomes]
rs10170604	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10173556	0.89[AFR][1000 genomes]
rs10175333	0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181650	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1035232	0.89[AFR][1000 genomes]
rs10865150	1.00[ASW][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap]
rs10865152	0.89[AFR][1000 genomes]
rs11124676	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs11124677	0.84[AFR][1000 genomes]
rs11124679	0.93[AFR][1000 genomes]
rs11124681	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12614034	0.82[AFR][1000 genomes]
rs12622941	0.83[YRI][hapmap]
rs12712641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13028561	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1468902	0.81[AFR][1000 genomes]
rs1474424	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1477164	0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1922827	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs2005892	0.87[AFR][1000 genomes]
rs2056654	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2111382	0.81[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2160661	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2178762	0.92[AFR][1000 genomes]
rs2193422	0.89[AFR][1000 genomes]
rs2373534	0.85[YRI][hapmap]
rs2373536	0.83[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2665157	0.91[ASW][hapmap];0.83[YRI][hapmap]
rs2708224	0.83[AMR][1000 genomes]
rs2888598	0.92[AFR][1000 genomes]
rs3755178	0.94[YRI][hapmap]
rs4670934	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670935	0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670936	0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6419603	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544222	0.90[AFR][1000 genomes]
rs6544228	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6717792	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6718134	0.83[AFR][1000 genomes]
rs6724393	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6730902	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6732611	0.88[AFR][1000 genomes]
rs6741312	0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742170	0.89[AFR][1000 genomes]
rs6743041	0.94[YRI][hapmap]
rs6756183	0.86[YRI][hapmap]
rs6759495	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6760382	0.89[AFR][1000 genomes]
rs7569834	0.91[ASW][hapmap]
rs7574785	1.00[MEX][hapmap]
rs7578136	0.87[AFR][1000 genomes]
rs7579414	0.83[AFR][1000 genomes]
rs7582160	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591102	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7595041	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7600014	0.83[ASW][hapmap]
rs7601700	1.00[ASW][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs7603392	0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7604047	0.82[AFR][1000 genomes]
rs7608153	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39592800-39617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:39600600-39614600	Weak transcription	Aorta	Aorta
5	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
6	chr2:39603400-39612000	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:39603400-39613200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
10	chr2:39604400-39610200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:39604600-39609600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:39604600-39610400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:39604600-39610800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:39605000-39609600	Enhancers	Rectal Smooth Muscle	rectum
15	chr2:39605000-39609800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:39605600-39609600	Enhancers	Brain Hippocampus Middle	brain
17	chr2:39605600-39612400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:39605800-39612200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:39606200-39609600	Enhancers	Osteobl	bone
20	chr2:39606200-39610400	Enhancers	Fetal Heart	heart
21	chr2:39606400-39610000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:39606400-39610000	Enhancers	Colon Smooth Muscle	Colon
23	chr2:39606400-39614000	Weak transcription	Right Ventricle	heart
24	chr2:39606600-39609800	Enhancers	NHLF	lung
25	chr2:39606600-39611800	Enhancers	HepG2	liver
26	chr2:39606800-39609800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr2:39606800-39610800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr2:39607000-39609600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr2:39607000-39626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:39607200-39614600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:39607400-39624800	Weak transcription	Stomach Mucosa	stomach
32	chr2:39607600-39610400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:39607600-39619800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:39607800-39609600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:39607800-39609600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:39607800-39609600	Enhancers	K562	blood
38	chr2:39607800-39610600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:39607800-39610800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:39608000-39612000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:39608000-39612000	Weak transcription	NHEK	skin
42	chr2:39608000-39622800	Weak transcription	Fetal Kidney	kidney
43	chr2:39608200-39610200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:39608200-39613000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:39608400-39609600	Enhancers	Duodenum Mucosa	Duodenum
46	chr2:39608400-39609800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:39608400-39612000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:39608400-39612200	Weak transcription	HMEC	breast
49	chr2:39608400-39612200	Weak transcription	HUVEC	blood vessel
50	chr2:39608400-39614600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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