Variant report

Variant	rs1228575
Chromosome Location	chr6:37009152-37009153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr6:37008533-37009580	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37005301..37010530-chr6:37136048..37140113,4	K562	blood:

Variant related genes	Relation type
COX6A1P2	TF binding region
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1224487	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1224488	0.88[ASN][1000 genomes]
rs1224491	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1724094	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1753300	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1753301	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025998	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094575	0.86[ASN][1000 genomes]
rs2149336	0.83[ASN][1000 genomes]
rs4317401	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711482	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457974	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457976	0.85[ASN][1000 genomes]
rs6457978	0.86[ASN][1000 genomes]
rs6457979	0.82[ASN][1000 genomes]
rs6924660	0.86[ASN][1000 genomes]
rs6939869	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748291	0.85[ASN][1000 genomes]
rs7750403	0.88[ASN][1000 genomes]
rs7750614	0.86[ASN][1000 genomes]
rs7750717	0.86[ASN][1000 genomes]
rs7770544	0.83[ASN][1000 genomes]
rs831484	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831487	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831489	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831491	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831497	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831499	0.97[ASN][1000 genomes]
rs831500	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831502	0.93[ASN][1000 genomes]
rs865550	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs913499	0.85[ASN][1000 genomes]
rs913500	0.93[ASN][1000 genomes]
rs913501	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296207	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296208	0.86[ASN][1000 genomes]
rs9366927	0.88[ASN][1000 genomes]
rs9380637	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394401	0.85[ASN][1000 genomes]
rs9394402	0.81[ASN][1000 genomes]
rs9394403	0.81[ASN][1000 genomes]
rs9462258	0.81[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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1228575	FGD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36993800-37018200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:36997400-37013800	Weak transcription	Esophagus	oesophagus
3	chr6:37000400-37015200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:37002000-37009200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr6:37002400-37014400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:37006800-37016200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:37006800-37016800	Weak transcription	Right Atrium	heart
8	chr6:37007800-37009600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:37007800-37015200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:37008000-37013800	Weak transcription	Pancreas	Pancrea
11	chr6:37008000-37015200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:37008000-37015600	Weak transcription	GM12878-XiMat	blood
13	chr6:37008200-37015400	Weak transcription	Primary B cells from cord blood	blood
14	chr6:37008400-37010000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:37008600-37010400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:37008600-37015000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:37008800-37009400	Enhancers	Dnd41	blood
18	chr6:37008800-37010000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr6:37009000-37009200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:37009000-37010800	Enhancers	K562	blood

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