Variant report

Variant	rs7741506
Chromosome Location	chr6:143951867-143951868
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12202402	0.83[AMR][1000 genomes]
rs12204134	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12211319	0.84[JPT][hapmap]
rs9321932	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9496713	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9496715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7741506	SAMD5	cis	parietal	SCAN
rs7741506	SF3B5	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143917000-143973600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:143939000-143955800	Weak transcription	Stomach Mucosa	stomach
3	chr6:143942200-143955600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:143947400-143955000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:143947400-143955200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr6:143947800-143955000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:143949800-143955000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:143950600-143953600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:143951200-143955600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:143951200-143960200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:143951600-143952000	Enhancers	Colon Smooth Muscle	Colon
12	chr6:143951800-143952000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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