Variant report

Variant	rs9689605
Chromosome Location	chr6:4103751-4103752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4101592..4105283-chr6:4133279..4135546,3	K562	blood:
2	chr6:4101592..4103959-chr6:4133279..4135546,2	K562	blood:

Variant related genes	Relation type
ENSG00000198721	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10085196	1.00[EUR][1000 genomes]
rs11759470	0.87[CEU][hapmap];1.00[GIH][hapmap]
rs13196680	0.87[CEU][hapmap];1.00[GIH][hapmap]
rs13197380	0.87[CEU][hapmap]
rs13200044	0.87[CEU][hapmap]
rs13205642	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13206444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13209389	0.87[CEU][hapmap]
rs13210282	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13210391	0.85[CEU][hapmap]
rs2326407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34094324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34200917	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs608917	0.89[EUR][1000 genomes]
rs622859	0.89[EUR][1000 genomes]
rs627902	0.89[EUR][1000 genomes]
rs6597030	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs715165	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs71553906	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7742642	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs853421	0.89[EUR][1000 genomes]
rs853422	0.88[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9328222	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9689605	F13A1	cis	parietal	SCAN
rs9689605	RREB1	cis	cerebellum	SCAN
rs9689605	PRPF4B	cis	parietal	SCAN
rs9689605	FOXF2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4100800-4104400	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr6:4101800-4110200	Weak transcription	Stomach Mucosa	stomach
3	chr6:4102600-4113800	Weak transcription	Psoas Muscle	Psoas
4	chr6:4102800-4103800	Flanking Active TSS	HepG2	liver
5	chr6:4103000-4103800	Enhancers	Fetal Intestine Small	intestine
6	chr6:4103000-4104600	Enhancers	Pancreas	Pancrea
7	chr6:4103000-4104600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:4103200-4104600	Enhancers	Fetal Brain Female	brain
9	chr6:4103400-4104200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:4103400-4109800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:4103400-4110000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:4103400-4115400	Weak transcription	Fetal Brain Male	brain
13	chr6:4103400-4115600	Weak transcription	Fetal Stomach	stomach
14	chr6:4103400-4115600	Weak transcription	Gastric	stomach
15	chr6:4103600-4104000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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