Variant report

Variant	rs12500115
Chromosome Location	chr4:78109837-78109838
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10005142	0.82[EUR][1000 genomes]
rs10009384	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs10016483	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10017014	0.81[EUR][1000 genomes]
rs10018359	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10020351	0.82[EUR][1000 genomes]
rs10026129	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10026646	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs10026795	0.82[EUR][1000 genomes]
rs10030867	0.82[EUR][1000 genomes]
rs10030957	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs10856957	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs11097729	0.83[EUR][1000 genomes]
rs11097730	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11097741	0.82[EUR][1000 genomes]
rs11724432	0.82[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs12504397	0.82[EUR][1000 genomes]
rs12508219	0.82[EUR][1000 genomes]
rs17397604	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28503908	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4150106	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs4285107	0.82[EUR][1000 genomes]
rs4302483	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4536958	0.82[EUR][1000 genomes]
rs4538513	0.82[EUR][1000 genomes]
rs4544732	0.83[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs4859475	0.82[EUR][1000 genomes]
rs4859751	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859752	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859753	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs4859754	0.82[EUR][1000 genomes]
rs4859755	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs4859758	0.82[EUR][1000 genomes]
rs55663411	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6532904	0.82[EUR][1000 genomes]
rs6840915	0.82[CEU][hapmap]
rs6849124	0.82[JPT][hapmap]
rs6849534	0.82[JPT][hapmap]
rs729240	0.84[EUR][1000 genomes]
rs7438755	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7690427	0.82[EUR][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:23 , 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	chr4:78099400-78111200	Weak transcription	NHEK	skin
3	chr4:78107400-78111200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:78108000-78110200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:78108000-78110200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:78108000-78111000	Enhancers	HSMMtube	muscle
7	chr4:78108000-78112000	Enhancers	Fetal Muscle Leg	muscle
8	chr4:78108200-78111400	Enhancers	Fetal Muscle Trunk	muscle
9	chr4:78108800-78110200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:78109000-78110000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:78109000-78110200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:78109000-78110200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:78109000-78113800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:78109000-78114000	Weak transcription	Thymus	Thymus
15	chr4:78109000-78114200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr4:78109000-78114200	Weak transcription	Fetal Thymus	thymus
17	chr4:78109000-78114400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr4:78109600-78110400	Enhancers	Brain Cingulate Gyrus	brain
19	chr4:78109600-78110600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:78109600-78110600	Enhancers	HSMM	muscle
21	chr4:78109600-78110800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:78109600-78112000	Enhancers	Fetal Intestine Large	intestine
23	chr4:78109800-78110000	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links