Variant report

Variant	rs9535646
Chromosome Location	chr13:51913708-51913709
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	chr13:51910169..51913793-chr13:51914133..51918271,3	K562	blood:

Variant related genes	Relation type
ENSG00000253309	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1028727	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17194948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17195020	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2408363	0.86[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4628860	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56017742	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73197809	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73197821	0.80[ASN][1000 genomes]
rs7321642	1.00[JPT][hapmap]
rs7328715	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7335122	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7335144	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7337450	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7989850	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs7998084	0.90[CEU][hapmap]
rs9316541	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9316545	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs9526757	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs9526758	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526759	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526761	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526764	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9535636	0.81[EUR][1000 genomes]
rs9535640	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9535644	0.86[EUR][1000 genomes]
rs9535652	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535655	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535660	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535661	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535662	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535663	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535665	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535670	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9535671	0.80[ASN][1000 genomes]
rs9535678	0.80[ASN][1000 genomes]
rs9535680	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9535682	0.80[ASN][1000 genomes]
rs9535696	0.90[CEU][hapmap]
rs9535697	0.90[CEU][hapmap]
rs9535699	1.00[CEU][hapmap]
rs9563046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568600	0.89[CEU][hapmap]
rs9568603	0.90[CEU][hapmap]
rs9568612	0.90[CEU][hapmap]
rs9634842	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9535646	INTS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51900200-51914000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:51900400-51938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr13:51905000-51913800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:51905400-51915200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:51906000-51917200	Weak transcription	HSMM	muscle
6	chr13:51906000-51944400	Weak transcription	Spleen	Spleen
7	chr13:51906200-51935400	Weak transcription	HSMMtube	muscle
8	chr13:51906800-51917200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr13:51907800-51933200	Weak transcription	Primary T cells from cord blood	blood
10	chr13:51909800-51917200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr13:51911000-51913800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:51911200-51920400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr13:51911800-51938600	Weak transcription	Pancreas	Pancrea
14	chr13:51912600-51916200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:51913400-51914000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:51913400-51914200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr13:51913400-51914200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr13:51913400-51915200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr13:51913400-51944600	Weak transcription	Aorta	Aorta
20	chr13:51913600-51914000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr13:51913600-51914200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr13:51913600-51914200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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