Variant report

Variant	rs9380590
Chromosome Location	chr6:36673510-36673511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36671517..36673727-chr6:36709746..36712131,2	K562	blood:
2	chr6:36670725..36674166-chr6:36726971..36730200,3	MCF-7	breast:
3	chr6:36562026..36564404-chr6:36670618..36673536,2	K562	blood:
4	chr6:36645661..36648559-chr6:36672946..36674521,2	K562	blood:

Variant related genes	Relation type
ENSG00000112081	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11750955	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11750982	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11753407	1.00[CEU][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12055620	0.82[JPT][hapmap]
rs12176359	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12526332	0.81[ASN][1000 genomes]
rs1972291	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236491	0.85[MEX][hapmap]
rs2395657	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395660	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2894409	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35442158	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72853397	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7756867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9349006	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9349007	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357223	0.85[MEX][hapmap]
rs9368955	0.85[EUR][1000 genomes]
rs9380589	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380591	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380592	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394373	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394374	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394376	1.00[EUR][1000 genomes];0.95[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	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv885808	chr6:36659932-36684518	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9380590	SRSF3	cis	parietal	SCAN
rs9380590	GRM4	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36661400-36696400	Weak transcription	Right Atrium	heart
2	chr6:36669800-36674000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:36669800-36675200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:36669800-36681400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:36670000-36675600	Weak transcription	Primary B cells from cord blood	blood
6	chr6:36670000-36682200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:36671000-36676200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:36671400-36682000	Weak transcription	Spleen	Spleen
9	chr6:36671800-36694000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr6:36672200-36681400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:36672200-36693600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:36672400-36679400	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links