Variant report

Variant	rs2104209
Chromosome Location	chr6:131622480-131622481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12203075	0.88[EUR][1000 genomes]
rs13211569	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1407533	0.88[EUR][1000 genomes]
rs3777478	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs3777483	0.83[TSI][hapmap]
rs3822866	0.81[CEU][hapmap]
rs4327722	0.88[EUR][1000 genomes]
rs61056763	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6569737	0.88[EUR][1000 genomes]
rs9483244	0.89[EUR][1000 genomes]
rs9483245	0.88[EUR][1000 genomes]
rs9800571	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv830808	chr6:131521115-131735320	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv886666	chr6:131573433-131666295	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv515476	chr6:131615425-132228577	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2104209	SNORD101	cis	parietal	SCAN
rs2104209	TAAR1	cis	parietal	SCAN
rs2104209	VNN1	cis	cerebellum	SCAN
rs2104209	TAAR9	cis	parietal	SCAN
rs2104209	TCF21	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131614800-131624800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr6:131615000-131623800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:131615000-131624400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:131615000-131626200	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:131618400-131630200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:131619200-131628600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:131619400-131630200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:131622200-131622600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:131622200-131622600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr6:131622200-131622600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:131622400-131622600	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
12	chr6:131622400-131622600	ZNF genes & repeats	Lung	lung
13	chr6:131622400-131622800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr6:131622400-131622800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
15	chr6:131622400-131622800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:131622400-131622800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:131622400-131622800	Enhancers	iPS DF 19.11 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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