Variant report

Variant	rs9379893
Chromosome Location	chr6:26584668-26584669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26170534..26173116-chr6:26582470..26585012,2	K562	blood:
2	chr6:26584191..26586044-chr6:27114721..27116358,2	K562	blood:
3	chr6:26575952..26578920-chr6:26582301..26585861,4	K562	blood:
4	chr6:26569360..26571169-chr6:26582823..26585671,2	K562	blood:
5	chr6:26575145..26580691-chr6:26582301..26587887,10	K562	blood:
6	chr6:26582641..26584492-chr6:26584652..26586344,2	MCF-7	breast:
7	chr6:26584544..26586590-chr6:27114721..27116911,2	K562	blood:
8	chr6:26583725..26585701-chr6:26603112..26605724,2	K562	blood:
9	chr6:26536187..26538587-chr6:26584341..26585867,2	K562	blood:
10	chr6:26581396..26586059-chr6:26589997..26593151,4	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF322-6	chr6:26584359-26585688	ucscGeneNc_uc003nie_1

No data

Variant related genes	Relation type
ENSG00000265565	Chromatin interaction
ENSG00000184825	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11967852	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11967935	0.83[AMR][1000 genomes]
rs13195210	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13208916	0.89[ASN][1000 genomes]
rs13210025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13214027	0.92[JPT][hapmap]
rs13215020	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16891725	0.92[JPT][hapmap]
rs16891790	1.00[CHB][hapmap]
rs16901784	0.92[JPT][hapmap]
rs2093169	0.92[JPT][hapmap]
rs28360517	0.89[ASN][1000 genomes]
rs3734544	0.92[JPT][hapmap]
rs3757150	0.92[JPT][hapmap]
rs3799383	0.92[JPT][hapmap]
rs3999471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4634439	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6920256	0.92[JPT][hapmap]
rs6936555	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6936561	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7740197	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7759969	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7773938	0.92[JPT][hapmap]
rs9295702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348726	0.89[ASN][1000 genomes]
rs9348727	0.86[CHB][hapmap]
rs9348728	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9358944	0.92[JPT][hapmap]
rs9358945	0.92[JPT][hapmap]
rs9358946	0.92[JPT][hapmap]
rs9366658	0.92[JPT][hapmap]
rs9368443	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368445	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368447	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368448	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368450	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368451	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9379895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379897	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9379899	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9379901	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs9379905	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393735	0.92[JPT][hapmap]
rs9393737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393739	0.84[EUR][1000 genomes];0.94[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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs9379893	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9379893	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs9379893	ZSCAN23	cis	cerebellum	SCAN
rs9379893	CMAH	cis	parietal	SCAN
rs9379893	BTN3A1	cis	lymphoblastoid	seeQTL
rs9379893	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs9379893	ZNF192	cis	cerebellum	SCAN
rs9379893	ZKSCAN3	cis	parietal	SCAN
rs9379893	ZSCAN23	cis	parietal	SCAN
rs9379893	HLA-A	cis	multi-tissue	Pritchard
rs9379893	BTN3A2	cis	lung	GTEx
rs9379893	BTN3A2	cis	lymphoblastoid	seeQTL
rs9379893	BTN3A3	cis	lymphoblastoid	seeQTL
rs9379893	BTN3A2	cis	Whole Blood	GTEx
rs9379893	BTN3A2	cis	multi-tissue	Pritchard
rs9379893	HIST1H2BH	cis	cerebellum	SCAN
rs9379893	HMGN4	cis	lymphoblastoid	seeQTL
rs9379893	HIST1H3A	cis	cerebellum	SCAN
rs9379893	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs9379893	LOC100270746	cis	lymphoblastoid	seeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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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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