Variant report

Variant	rs12504397
Chromosome Location	chr4:78113726-78113727
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	chr22:45918563..45921114-chr4:78111513..78114166,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10005142	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10009384	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10010290	0.97[ASN][1000 genomes]
rs10017014	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10018359	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10020351	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10026129	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10026795	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10030727	0.82[EUR][1000 genomes]
rs10030735	0.82[EUR][1000 genomes]
rs10030867	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10030957	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10856957	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097728	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097729	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097730	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097741	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12500115	0.82[EUR][1000 genomes]
rs12508219	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1559119	0.81[ASN][1000 genomes]
rs1559122	0.82[ASN][1000 genomes]
rs17397604	0.84[EUR][1000 genomes]
rs1968235	0.81[ASN][1000 genomes]
rs2042228	0.81[ASN][1000 genomes]
rs28503908	0.84[EUR][1000 genomes]
rs4285107	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4504280	0.80[ASN][1000 genomes]
rs4536958	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4538513	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4582179	0.96[ASN][1000 genomes]
rs4582180	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859475	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859477	0.82[ASN][1000 genomes]
rs4859751	0.84[EUR][1000 genomes]
rs4859752	0.91[EUR][1000 genomes]
rs4859753	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859754	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859755	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859758	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55663411	0.84[EUR][1000 genomes]
rs6532904	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6532919	0.81[ASN][1000 genomes]
rs6532921	0.83[ASN][1000 genomes]
rs6822794	0.81[ASN][1000 genomes]
rs6838744	0.81[ASN][1000 genomes]
rs6840915	0.82[EUR][1000 genomes]
rs6844009	0.81[ASN][1000 genomes]
rs6857792	0.82[EUR][1000 genomes]
rs7438755	0.80[EUR][1000 genomes]
rs7690427	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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	nsv879500	chr4:78045960-78115334	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1000730	chr4:78109138-78210296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr4:78094400-78114200	Weak transcription	Primary B cells from cord blood	blood
2	chr4:78109000-78113800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr4:78109000-78114000	Weak transcription	Thymus	Thymus
4	chr4:78109000-78114200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr4:78109000-78114200	Weak transcription	Fetal Thymus	thymus
6	chr4:78109000-78114400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:78110400-78114200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:78110400-78114200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:78112000-78114200	Weak transcription	Placenta	Placenta
10	chr4:78112000-78114800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:78112000-78116200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:78112000-78117400	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:78112000-78120600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:78112200-78120600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:78113400-78113800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:78113600-78118600	Weak transcription	NHEK	skin
17	chr4:78113600-78120400	Weak transcription	HMEC	breast

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