Variant report

Variant	rs1541871
Chromosome Location	chr3:116102816-116102817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12491423	1.00[JPT][hapmap]
rs1619655	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17646258	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1835674	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1920185	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1920191	0.91[YRI][hapmap]
rs2163504	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4521220	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6785974	0.85[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs724115	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627104	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648197	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845203	1.00[CHB][hapmap]
rs9852860	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs9856796	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs988803	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877361	chr3:116017931-116138039	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv437338	chr3:116076289-116110635	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2757005	chr3:116085678-116121948	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv2759170	chr3:116085678-116121948	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1014989	chr3:116096198-116109192	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1003543	chr3:116096198-116111430	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3463484	chr3:116098674-116110408	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3463485	chr3:116098674-116110408	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv21066	chr3:116098946-116109977	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv516570	chr3:116099041-116108165	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1011591	chr3:116099041-116109192	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541871	GRAMD1C	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116096400-116108000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:116102200-116104200	Enhancers	Brain Substantia Nigra	brain
3	chr3:116102600-116103000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:116102600-116103000	Enhancers	Fetal Lung	lung
5	chr3:116102600-116103200	Enhancers	Rectal Smooth Muscle	rectum
6	chr3:116102600-116103600	Enhancers	Brain Hippocampus Middle	brain
7	chr3:116102600-116103800	Enhancers	Brain Germinal Matrix	brain
8	chr3:116102600-116104400	Enhancers	Brain Anterior Caudate	brain
9	chr3:116102800-116103000	Enhancers	Fetal Brain Male	brain
10	chr3:116102800-116103200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:116102800-116103800	Enhancers	Brain Angular Gyrus	brain
12	chr3:116102800-116103800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:116102800-116104200	Enhancers	Colon Smooth Muscle	Colon

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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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