Variant report

Variant	rs9378431
Chromosome Location	chr6:5580951-5580952
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1124339	0.80[CHB][hapmap]
rs4573125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[ASN][1000 genomes]
rs55735025	0.96[ASN][1000 genomes]
rs55943047	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6927274	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7744150	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744285	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7751224	0.96[ASN][1000 genomes]
rs7767977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7768379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[ASN][1000 genomes]
rs9378430	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9378433	0.81[CHB][hapmap]
rs9378967	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9378968	1.00[ASW][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9392700	0.81[CHB][hapmap]
rs9405851	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv883420	chr6:5524393-5584422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv5181	chr6:5536921-5581595	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1016905	chr6:5566364-5639167	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv981213	chr6:5578587-5582864	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9378431	DSP	cis	parietal	SCAN
rs9378431	SLC22A23	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5565200-5583200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:5574200-5583400	Weak transcription	NHDF-Ad	bronchial
3	chr6:5576200-5581400	Weak transcription	Primary B cells from cord blood	blood
4	chr6:5577400-5639800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:5578200-5584200	Weak transcription	Fetal Lung	lung
6	chr6:5580600-5582000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:5580800-5581000	Enhancers	Gastric	stomach
8	chr6:5580800-5581000	Enhancers	Lung	lung
9	chr6:5580800-5581000	Enhancers	Spleen	Spleen
10	chr6:5580800-5581600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:5580800-5581600	Enhancers	Primary T cells from cord blood	blood
12	chr6:5580800-5581800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr6:5580800-5581800	Enhancers	Fetal Muscle Leg	muscle
14	chr6:5580800-5582000	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:5580800-5582000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr6:5580800-5582200	Enhancers	Fetal Thymus	thymus
17	chr6:5580800-5582800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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