Variant report

Variant	rs1952435
Chromosome Location	chr6:70095690-70095691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1283467	0.86[CEU][hapmap];0.89[YRI][hapmap]
rs1283470	0.90[YRI][hapmap]
rs1290329	0.94[GIH][hapmap];0.90[YRI][hapmap]
rs1328735	0.81[ASW][hapmap];0.80[LWK][hapmap]
rs16900676	0.87[CHD][hapmap]
rs2149457	0.94[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3799094	0.81[CHD][hapmap]
rs7745125	0.81[ASW][hapmap];0.82[CEU][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];0.80[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs7749882	0.97[GIH][hapmap];0.80[TSI][hapmap];0.90[YRI][hapmap]
rs913537	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9351751	0.87[CHD][hapmap]
rs9454732	0.94[GIH][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886137	chr6:69684850-70095690	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv432919	chr6:69873179-70221322	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv463149	chr6:70007450-70097588	Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv603635	chr6:70007450-70097588	Weak transcription Enhancers Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1952435	BAI3	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70054600-70098600	Weak transcription	Brain Anterior Caudate	brain
2	chr6:70054600-70100600	Weak transcription	Brain Angular Gyrus	brain
3	chr6:70081000-70108000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:70082200-70098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:70088200-70099600	Weak transcription	Small Intestine	intestine
6	chr6:70092600-70100200	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:70093600-70096000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:70093800-70095800	Enhancers	Brain Germinal Matrix	brain
9	chr6:70094200-70096000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:70094600-70095800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:70094600-70098400	Weak transcription	Fetal Lung	lung
12	chr6:70095200-70096000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:70095400-70095800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr6:70095400-70096200	Weak transcription	Fetal Brain Male	brain
15	chr6:70095600-70096000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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