Variant report

Variant	rs3777612
Chromosome Location	chr6:45965608-45965609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1338470	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1338471	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1361216	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1416170	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1535108	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2022419	0.92[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2894658	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711840	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4714900	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458479	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs6458480	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs6458481	0.88[ASN][1000 genomes]
rs6458482	0.88[ASN][1000 genomes]
rs6458483	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6921959	0.88[ASN][1000 genomes]
rs7772905	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7773297	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395142	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9472651	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9472653	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9689698	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv428482	chr6:45926644-46050182	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv885867	chr6:45936223-45982976	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1025846	chr6:45955173-46047269	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3777612	POLR1C	cis	parietal	SCAN
rs3777612	TRERF1	cis	parietal	SCAN
rs3777612	TNFRSF21	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45956800-45969000	Weak transcription	Fetal Intestine Small	intestine
2	chr6:45957000-45966000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:45957000-45969000	Weak transcription	Spleen	Spleen
4	chr6:45957000-45977400	Weak transcription	Fetal Intestine Large	intestine
5	chr6:45960400-45970400	Weak transcription	Small Intestine	intestine
6	chr6:45965400-45966000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr6:45965400-45966000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:45965400-45966400	Enhancers	Fetal Heart	heart
9	chr6:45965600-45965800	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr6:45965600-45966200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:45965600-45966200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr6:45965600-45966600	Enhancers	Fetal Muscle Leg	muscle
13	chr6:45965600-45966600	Enhancers	Placenta	Placenta
14	chr6:45965600-45967000	Enhancers	Left Ventricle	heart
15	chr6:45965600-45967000	Enhancers	Psoas Muscle	Psoas
16	chr6:45965600-45967000	Enhancers	Right Ventricle	heart

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