Variant report

Variant	rs7769351
Chromosome Location	chr6:53827853-53827854
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10456168	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10456676	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10755768	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10948790	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12190914	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13437448	0.94[ASN][1000 genomes]
rs2006013	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050159	0.80[EUR][1000 genomes]
rs2206574	0.82[ASN][1000 genomes]
rs2397150	0.82[ASN][1000 genomes]
rs34299171	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4398734	0.86[ASN][1000 genomes]
rs4712050	0.89[ASN][1000 genomes]
rs4712051	0.90[ASN][1000 genomes]
rs5006063	0.95[ASN][1000 genomes]
rs6458973	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6902746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906326	0.81[CEU][hapmap]
rs6907354	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6909052	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6909056	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6909350	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6927232	0.92[ASN][1000 genomes]
rs6928440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935942	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs742525	0.86[ASN][1000 genomes]
rs7744962	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7752981	0.82[ASN][1000 genomes]
rs7773779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296727	0.94[ASN][1000 genomes]
rs9357777	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9357779	0.81[ASN][1000 genomes]
rs9367545	0.91[AMR][1000 genomes]
rs9367546	0.82[ASN][1000 genomes]
rs9370245	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9395890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9395891	1.00[CEU][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9395892	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9395893	0.86[ASN][1000 genomes]
rs9395894	0.86[ASN][1000 genomes]
rs9463996	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs9463997	0.81[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7769351	LRRC1	cis	parietal	SCAN
rs7769351	DEFB110	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53826200-53828400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:53826600-53828200	Enhancers	Fetal Heart	heart
3	chr6:53826800-53828200	Enhancers	Fetal Muscle Leg	muscle
4	chr6:53827400-53828200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:53827400-53828200	Enhancers	HSMMtube	muscle
6	chr6:53827400-53832000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:53827400-53832200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:53827400-53832200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:53827400-53836000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:53827400-53836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:53827600-53828200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr6:53827800-53828200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr6:53827800-53832000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:53827800-53836000	Weak transcription	Psoas Muscle	Psoas

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