Variant report

Variant	rs10484654
Chromosome Location	chr6:53882737-53882738
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10484651	0.86[CHD][hapmap]
rs10484652	0.86[CHD][hapmap]
rs10484653	0.86[CHD][hapmap]
rs11961988	0.86[CHD][hapmap]
rs12193439	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206659	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12210600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409105	0.96[AFR][1000 genomes]
rs1570912	0.83[CHD][hapmap]
rs16884583	0.86[CHD][hapmap]
rs4142190	0.96[AFR][1000 genomes]
rs9296731	0.85[CHB][hapmap];0.96[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1018062	chr6:53842588-53925192	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv5307	chr6:53874118-53952230	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10484654	KIAA1586	cis	parietal	SCAN
rs10484654	COL21A1	cis	cerebellum	SCAN
rs10484654	C6orf142	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53875600-53883600	Weak transcription	Left Ventricle	heart
2	chr6:53876400-53883400	Weak transcription	Right Atrium	heart
3	chr6:53879600-53883400	Weak transcription	Psoas Muscle	Psoas
4	chr6:53880200-53883200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:53881200-53883400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:53881400-53883000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:53881400-53883400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:53881600-53883600	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:53882200-53883000	Enhancers	HSMMtube	muscle
10	chr6:53882200-53883200	Enhancers	Fetal Heart	heart
11	chr6:53882200-53884000	Enhancers	HSMM	muscle
12	chr6:53882200-53887400	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr6:53882400-53882800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:53882400-53883800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:53882600-53885800	Enhancers	Liver	Liver

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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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