Variant report

Variant	rs4532541
Chromosome Location	chr7:104457800-104457801
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10953453	0.90[CHB][hapmap];0.90[YRI][hapmap]
rs11762138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764774	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12667640	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2192931	0.90[CHB][hapmap];0.86[YRI][hapmap]
rs2385466	0.90[CHB][hapmap]
rs4266569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4382394	0.90[CHB][hapmap];0.90[YRI][hapmap]
rs4730052	0.90[YRI][hapmap]
rs4730053	0.90[YRI][hapmap]
rs6466028	0.90[CHB][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429790	chr7:104314049-104488049	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv429792	chr7:104400049-104488049	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5887	chr7:104401250-104491604	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030875	chr7:104409391-104472647	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1028479	chr7:104409391-104479087	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv528392	chr7:104411273-104466675	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv522743	chr7:104411273-104486707	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv831086	chr7:104422503-104596766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1019625	chr7:104429371-104461487	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4532541	FAM185A	cis	cerebellum	SCAN
rs4532541	BAIAP2	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104440400-104482400	Weak transcription	Fetal Intestine Small	intestine
2	chr7:104448600-104459800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:104453000-104459200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr7:104455800-104459600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:104455800-104460200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:104455800-104460800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:104456600-104460600	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:104457400-104461600	Weak transcription	Brain Anterior Caudate	brain
9	chr7:104457600-104458400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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Input of quick search could be:

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

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