Variant report

Variant	rs1990610
Chromosome Location	chr2:40666926-40666927
allele	C/G
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: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10164458	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs1990609	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2373860	1.00[JPT][hapmap]
rs4245783	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4411757	0.82[AFR][1000 genomes]
rs4450659	0.82[EUR][1000 genomes]
rs4557029	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs4952414	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4952620	0.89[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6544339	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6719806	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6719986	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs6726520	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6737745	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6749800	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7349326	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7603114	1.00[YRI][hapmap];0.84[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	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

No data

Chromatin state (count:37 , 50 per page) page: 1

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	chr2:40657000-40671200	Weak transcription	Fetal Stomach	stomach
6	chr2:40662600-40667800	Weak transcription	Primary B cells from cord blood	blood
7	chr2:40662600-40677200	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:40663400-40672000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:40663600-40677000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:40663600-40677000	Weak transcription	Aorta	Aorta
11	chr2:40663800-40667800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:40663800-40677600	Weak transcription	HSMMtube	muscle
13	chr2:40664000-40667000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:40664200-40667400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr2:40664200-40667800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:40664400-40667200	Enhancers	NHDF-Ad	bronchial
17	chr2:40664600-40667600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:40664600-40673000	Weak transcription	Left Ventricle	heart
19	chr2:40665000-40667000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:40665000-40668200	Enhancers	Osteobl	bone
21	chr2:40665200-40667800	Enhancers	HSMM	muscle
22	chr2:40665200-40668400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:40665200-40668600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:40665200-40675200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:40665400-40674800	Weak transcription	NHLF	lung
26	chr2:40665800-40668000	Weak transcription	Dnd41	blood
27	chr2:40666000-40667000	Enhancers	Brain Anterior Caudate	brain
28	chr2:40666000-40667000	Enhancers	HMEC	breast
29	chr2:40666200-40667000	Enhancers	NHEK	skin
30	chr2:40666600-40673400	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:40666600-40676400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:40666600-40676600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:40666600-40677200	Weak transcription	Right Ventricle	heart
34	chr2:40666800-40667000	Flanking Active TSS	Fetal Heart	heart
35	chr2:40666800-40667000	Enhancers	NH-A	brain
36	chr2:40666800-40671200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:40666800-40675400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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