Variant report

Variant	rs2699992
Chromosome Location	chr12:44278013-44278014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:44228150..44229800-chr12:44275974..44278416,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139173	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10736017	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10748373	0.88[ASN][1000 genomes]
rs12298970	0.88[ASN][1000 genomes]
rs12311962	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12314126	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1675765	1.00[CHB][hapmap]
rs1675766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1675771	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1675774	0.83[ASN][1000 genomes]
rs1675776	0.81[ASN][1000 genomes]
rs1675778	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1675782	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1675783	0.88[ASN][1000 genomes]
rs1675784	0.88[ASN][1000 genomes]
rs1675786	0.88[ASN][1000 genomes]
rs1675788	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1675791	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1731422	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1731427	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1731429	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1731438	0.88[ASN][1000 genomes]
rs1731439	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1731440	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1731442	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1731447	0.80[AFR][1000 genomes]
rs1731449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1731453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447114	0.88[ASN][1000 genomes]
rs2447115	0.88[ASN][1000 genomes]
rs2447116	0.83[ASN][1000 genomes]
rs2614394	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2951436	0.88[ASN][1000 genomes]
rs4238090	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4354753	1.00[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4768049	0.88[ASN][1000 genomes]
rs4768052	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs73098836	0.88[ASN][1000 genomes]
rs7953229	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957146	0.82[ASN][1000 genomes]
rs7958314	0.82[ASN][1000 genomes]
rs7965635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966024	0.82[ASN][1000 genomes]

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	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899048	chr12:44209423-44307888	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44240400-44293000	Weak transcription	Aorta	Aorta
2	chr12:44256400-44285600	Weak transcription	HSMMtube	muscle
3	chr12:44273800-44278400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:44274600-44278600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:44274600-44286000	Weak transcription	Pancreas	Pancrea
6	chr12:44275000-44278400	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:44275000-44281200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:44276600-44278600	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr12:44276800-44278400	Weak transcription	Brain Anterior Caudate	brain
10	chr12:44276800-44278600	Enhancers	Osteobl	bone
11	chr12:44277000-44278600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:44277000-44279600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:44277200-44278600	Enhancers	HMEC	breast
14	chr12:44277600-44278600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:44277800-44278200	Weak transcription	Left Ventricle	heart
16	chr12:44277800-44278600	Weak transcription	Esophagus	oesophagus
17	chr12:44277800-44279600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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