Variant report

Variant	rs73003138
Chromosome Location	chr2:134267191-134267192
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	chr2:134265911..134268884-chr2:134269496..134274997,4	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1016837	0.88[AMR][1000 genomes]
rs1017366	0.81[EUR][1000 genomes]
rs11891880	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11903204	0.81[EUR][1000 genomes]
rs16826050	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16826052	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60316439	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61578634	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720995	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6730679	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6732077	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990470	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990471	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990476	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990483	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990486	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990490	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990493	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990494	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72992306	0.81[EUR][1000 genomes]
rs72992325	0.81[EUR][1000 genomes]
rs72992334	0.81[EUR][1000 genomes]
rs72992339	0.81[EUR][1000 genomes]
rs72992347	0.81[EUR][1000 genomes]
rs72992351	0.81[EUR][1000 genomes]
rs72992377	0.81[EUR][1000 genomes]
rs73003136	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73003141	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003144	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003146	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003147	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7340446	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7340510	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917399	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2830192	chr2:134259612-134311713	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134262000-134267600	Enhancers	Brain Germinal Matrix	brain
2	chr2:134262600-134267400	Weak transcription	Esophagus	oesophagus
3	chr2:134263200-134268600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:134264200-134268200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:134264400-134267600	Enhancers	Brain Substantia Nigra	brain
6	chr2:134264800-134267600	Enhancers	Brain Hippocampus Middle	brain
7	chr2:134265000-134267200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:134265200-134267200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:134265200-134267400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:134265600-134267400	Enhancers	Fetal Brain Male	brain
11	chr2:134265600-134267800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:134266200-134267200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:134266800-134267400	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:134266800-134267600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:134266800-134268000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:134266800-134270600	Weak transcription	Brain Anterior Caudate	brain
17	chr2:134266800-134271000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:134266800-134273000	Weak transcription	Brain Angular Gyrus	brain
19	chr2:134266800-134273800	Weak transcription	Fetal Brain Female	brain
20	chr2:134267000-134267200	Enhancers	Placenta	Placenta
21	chr2:134267000-134267800	Enhancers	HMEC	breast
22	chr2:134267000-134267800	Enhancers	NHEK	skin
23	chr2:134267000-134275200	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links