Variant report

Variant	rs4388976
Chromosome Location	chr12:105280650-105280651
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	chr12:105279433..105282417-chr12:105292358..105295004,2	MCF-7	breast:
2	chr12:105280491..105282249-chr12:105345116..105347346,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136052	Chromatin interaction
ENSG00000265054	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1002803	0.90[CHB][hapmap]
rs10507184	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10746008	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10778355	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10778358	0.90[CHB][hapmap];0.93[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861294	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861296	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11112253	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1155994	0.85[ASN][1000 genomes]
rs1389612	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1565813	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2248012	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2248986	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2249454	0.90[CHB][hapmap];0.93[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2264892	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2453156	0.95[CHB][hapmap]
rs2453160	0.83[ASN][1000 genomes]
rs2453166	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2463018	0.95[CHB][hapmap]
rs2463440	0.85[CHB][hapmap]
rs2468092	0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2468099	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs2468100	0.85[ASN][1000 genomes]
rs2468105	0.95[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2468337	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468340	0.85[ASN][1000 genomes]
rs2730291	0.90[CHB][hapmap]
rs4334113	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4393404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964310	0.87[JPT][hapmap]
rs6539170	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6539171	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7135015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7138686	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7309240	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73193606	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7967503	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968763	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7980681	0.87[ASN][1000 genomes]
rs9668618	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105267800-105284200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:105273800-105288200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:105275400-105297000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:105276400-105281800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:105278200-105281000	Enhancers	Fetal Lung	lung
6	chr12:105278200-105284400	Weak transcription	Aorta	Aorta
7	chr12:105278200-105284400	Weak transcription	Gastric	stomach
8	chr12:105278400-105293200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:105278600-105281600	Enhancers	Hela-S3	cervix
10	chr12:105278600-105313800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:105279600-105280800	Enhancers	HUVEC	blood vessel
12	chr12:105279600-105281200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr12:105280000-105280800	Flanking Active TSS	A549	lung
14	chr12:105280200-105280800	Enhancers	NHEK	skin
15	chr12:105280400-105281800	Weak transcription	Liver	Liver
16	chr12:105280600-105280800	Weak transcription	Osteobl	bone
17	chr12:105280600-105284400	Weak transcription	NHDF-Ad	bronchial

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