Variant report

Variant	rs3798267
Chromosome Location	chr6:45950827-45950828
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1204337	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1209539	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1212565	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777601	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs4714897	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4714898	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4714899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59001937	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62400483	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72856960	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472642	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3798267	CLIC5	cis	cerebellum	SCAN
rs3798267	CAPN11	cis	cerebellum	SCAN
rs3798267	MRPL14	cis	cerebellum	SCAN
rs3798267	CLIC5	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45938600-45953200	Weak transcription	Lung	lung
2	chr6:45943400-45952600	Weak transcription	Placenta	Placenta
3	chr6:45946600-45954800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr6:45946800-45952600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr6:45947200-45951000	Weak transcription	Right Atrium	heart
6	chr6:45949200-45951600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr6:45949400-45954600	Weak transcription	Fetal Kidney	kidney
8	chr6:45949800-45951400	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr6:45950400-45951200	Enhancers	Duodenum Mucosa	Duodenum
10	chr6:45950600-45951000	Enhancers	Fetal Heart	heart
11	chr6:45950600-45951200	Enhancers	Fetal Intestine Small	intestine
12	chr6:45950600-45960200	Enhancers	Psoas Muscle	Psoas
13	chr6:45950800-45951000	Genic enhancers	Right Ventricle	heart
14	chr6:45950800-45951200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:45950800-45951400	Genic enhancers	Fetal Intestine Large	intestine
16	chr6:45950800-45951400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr6:45950800-45951400	Enhancers	Small Intestine	intestine
18	chr6:45950800-45953400	Genic enhancers	Left Ventricle	heart

Quick Search:

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

what's new

Quick links