Variant report

Variant	rs4629203
Chromosome Location	chr2:40662546-40662547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40662045..40663958-chr2:40665740..40668580,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11685475	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11901878	0.80[JPT][hapmap]
rs12052649	0.81[CHB][hapmap]
rs12052650	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12052800	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12988659	0.81[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs13017237	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs13023706	0.82[ASN][1000 genomes]
rs17025965	0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs17026033	0.82[MKK][hapmap];0.85[YRI][hapmap]
rs34528721	0.84[ASN][1000 genomes]
rs35129449	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952621	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs6712702	0.80[JPT][hapmap]
rs6742589	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7579930	0.82[ASN][1000 genomes]
rs9789737	0.80[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9789739	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]

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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40646600-40670800	Weak transcription	Fetal Brain Female	brain
2	chr2:40648000-40667200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:40648200-40676400	Weak transcription	Fetal Kidney	kidney
4	chr2:40653000-40674800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:40655000-40665000	Weak transcription	Fetal Brain Male	brain
6	chr2:40657000-40671200	Weak transcription	Fetal Stomach	stomach
7	chr2:40657800-40663000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:40657800-40666600	Enhancers	Colon Smooth Muscle	Colon
9	chr2:40658000-40663600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:40658000-40664000	Enhancers	NHDF-Ad	bronchial
11	chr2:40658000-40664200	Enhancers	HMEC	breast
12	chr2:40658200-40663400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:40658200-40663600	Enhancers	Osteobl	bone
14	chr2:40658200-40665400	Enhancers	NHLF	lung
15	chr2:40658400-40663600	Enhancers	Adipose Nuclei	Adipose
16	chr2:40658600-40663400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:40658600-40663800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:40658800-40662800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:40659200-40663400	Enhancers	Hela-S3	cervix
20	chr2:40659600-40663200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:40659800-40664000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:40659800-40665600	Weak transcription	Dnd41	blood
23	chr2:40660000-40663200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:40660200-40663400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:40660200-40663400	Enhancers	HSMM	muscle
26	chr2:40660600-40663800	Enhancers	HUVEC	blood vessel
27	chr2:40660800-40663600	Enhancers	Aorta	Aorta
28	chr2:40660800-40664600	Enhancers	Left Ventricle	heart
29	chr2:40661000-40664600	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr2:40661600-40662800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr2:40661600-40662800	Flanking Active TSS	A549	lung
32	chr2:40661600-40663000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:40661600-40663600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:40661800-40662800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr2:40661800-40662800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr2:40661800-40662800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:40661800-40663400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:40661800-40666000	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:40662000-40662600	Enhancers	Fetal Muscle Leg	muscle
40	chr2:40662000-40662600	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr2:40662000-40662800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr2:40662000-40662800	Enhancers	Right Atrium	heart
43	chr2:40662000-40663200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:40662000-40663400	Enhancers	Placenta	Placenta
45	chr2:40662000-40663600	Enhancers	Brain Anterior Caudate	brain
46	chr2:40662200-40662800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:40662200-40663200	Enhancers	Fetal Heart	heart
48	chr2:40662200-40663800	Enhancers	NHEK	skin
49	chr2:40662200-40665800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:40662400-40662600	Enhancers	Primary B cells from cord blood	blood

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