Variant report

Variant	rs4257060
Chromosome Location	chr12:105344381-105344382
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	chr12:105343851..105348812-chr12:105350003..105354386,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136052	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10507183	0.82[ASN][1000 genomes]
rs10507185	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10778354	0.86[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10778356	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861278	0.81[ASN][1000 genomes]
rs10861282	0.89[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861291	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861293	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861295	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861297	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112208	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11112221	0.82[ASN][1000 genomes]
rs11112234	0.86[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12230637	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs17829927	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2245695	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249941	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2252843	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2264883	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2264893	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453163	0.82[ASN][1000 genomes]
rs2453164	0.82[ASN][1000 genomes]
rs2468096	0.81[ASN][1000 genomes]
rs2468098	0.81[ASN][1000 genomes]
rs2468103	0.82[ASN][1000 genomes]
rs2468107	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2468108	0.82[ASN][1000 genomes]
rs2468336	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2468338	0.83[JPT][hapmap]
rs2468339	0.89[JPT][hapmap]
rs2468341	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2468343	0.82[ASN][1000 genomes]
rs2468396	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2468397	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2642119	0.82[ASN][1000 genomes]
rs2642120	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2730294	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs3890816	0.96[CEU][hapmap]
rs4130161	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4409923	0.89[CEU][hapmap]
rs4537841	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4630370	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4644704	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57987047	0.90[EUR][1000 genomes]
rs7959777	0.89[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7961766	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7971260	0.82[ASN][1000 genomes]
rs7971392	0.83[ASN][1000 genomes]
rs9705471	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105333200-105346200	Weak transcription	HepG2	liver
2	chr12:105338200-105349000	Weak transcription	Pancreas	Pancrea
3	chr12:105338200-105351000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:105338400-105346600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:105342600-105350600	Weak transcription	Adipose Nuclei	Adipose
6	chr12:105342800-105345200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:105342800-105345200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:105342800-105346000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:105342800-105346000	Weak transcription	Small Intestine	intestine
10	chr12:105343400-105345200	Enhancers	Stomach Mucosa	stomach
11	chr12:105344200-105344400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:105344200-105346600	Enhancers	Liver	Liver

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