Variant report

Variant	rs6563698
Chromosome Location	chr13:39934077-39934078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2025410	0.90[EUR][1000 genomes]
rs2147130	0.81[JPT][hapmap]
rs2181760	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324258	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2985186	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7318557	0.82[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7990125	0.81[JPT][hapmap]
rs9285131	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9315678	0.82[GIH][hapmap]
rs9315679	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv996813	chr13:39929705-39937070	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	lncRNA	n/a	inside rSNPs	diseases
5	esv3506174	chr13:39932452-39937350	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv3497338	chr13:39933102-39936550	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
7	esv3506185	chr13:39933377-39936825	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
8	esv3497336	chr13:39933552-39936600	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
9	esv21149	chr13:39933627-39935387	Weak transcription	n/a	n/a	inside rSNPs	diseases
10	nsv826624	chr13:39933627-39935533	Weak transcription	n/a	n/a	inside rSNPs	diseases
11	esv3497337	chr13:39933688-39937250	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3506207	chr13:39933778-39936097	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
13	nsv820008	chr13:39934001-39935574	Weak transcription	n/a	n/a	inside rSNPs	diseases
14	esv3506196	chr13:39934002-39936000	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
15	esv3506218	chr13:39934055-39935602	Weak transcription	n/a	n/a	inside rSNPs	diseases
16	esv3497335	chr13:39934071-39935581	Weak transcription	n/a	n/a	inside rSNPs	diseases
17	nsv561532	chr13:39934077-39935150	Weak transcription	n/a	n/a	inside rSNPs	diseases
18	nsv511518	chr13:39934077-39936903	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6563698	LHFP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39925200-39936800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr13:39925200-39938600	Weak transcription	Aorta	Aorta
3	chr13:39928400-39936400	Weak transcription	Left Ventricle	heart
4	chr13:39928400-39939000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr13:39928400-39939000	Weak transcription	Right Atrium	heart
6	chr13:39928800-39938800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:39929200-39938800	Weak transcription	Fetal Heart	heart
8	chr13:39933600-39936400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:39933800-39937000	Weak transcription	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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