Variant report

Variant	rs2022419
Chromosome Location	chr6:45973511-45973512
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1338470	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1338471	0.82[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1361216	0.94[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs1416170	0.82[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1535108	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2894658	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3777612	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]
rs4711840	0.82[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4714900	0.85[ASN][1000 genomes]
rs6458479	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs6458480	0.94[CHB][hapmap]
rs6458483	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772905	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7773297	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9395142	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9472651	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9472653	0.81[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9689698	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2022419	POLR1C	cis	parietal	SCAN
rs2022419	TNFRSF21	cis	parietal	SCAN
rs2022419	TRERF1	cis	parietal	SCAN
rs2022419	CLIC5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45957000-45977400	Weak transcription	Fetal Intestine Large	intestine
2	chr6:45966200-45978200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:45967800-45976600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr6:45968000-45979400	Enhancers	Right Ventricle	heart
5	chr6:45968600-45975000	Enhancers	Psoas Muscle	Psoas
6	chr6:45969000-45978000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:45969200-45978400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr6:45969400-45976000	Weak transcription	Lung	lung
9	chr6:45969400-45978800	Weak transcription	Spleen	Spleen
10	chr6:45970200-45977400	Enhancers	Left Ventricle	heart
11	chr6:45970600-45978200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:45970800-45975200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:45971000-45977600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:45972000-45975600	Strong transcription	Fetal Intestine Small	intestine
15	chr6:45972400-45974400	Weak transcription	Fetal Heart	heart
16	chr6:45973200-45981600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:45973400-45974400	Weak transcription	Right Atrium	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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