Variant report

Variant	rs10972438
Chromosome Location	chr9:3542092-3542093
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:3525260..3527917-chr9:3541614..3544234,2	MCF-7	breast:
2	chr9:3541273..3543757-chr9:3545935..3548422,2	K562	blood:
3	chr9:3525195..3528212-chr9:3542053..3545804,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232104	Chromatin interaction
ENSG00000080298	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10115088	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10118702	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10758299	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10814219	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10814233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10814235	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10814250	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10814251	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10972435	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1133463	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1133467	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12004862	0.83[EUR][1000 genomes]
rs12684702	0.92[ASN][1000 genomes]
rs2027089	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28510559	0.85[EUR][1000 genomes]
rs3954945	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7022948	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7027862	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7041399	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7042747	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7045092	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7847562	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7858486	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7864107	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7867083	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7871094	0.86[ASN][1000 genomes]
rs7871777	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7873538	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9774864	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9792451	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10972438	RP11-509J21.1	cis	Artery Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3527400-3567600	Weak transcription	Ovary	ovary
2	chr9:3528200-3550400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:3528600-3554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:3528800-3553600	Weak transcription	Adipose Nuclei	Adipose
5	chr9:3528800-3560600	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:3529000-3579000	Weak transcription	HSMMtube	muscle
7	chr9:3529200-3548400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:3529200-3550800	Weak transcription	Primary B cells from cord blood	blood
9	chr9:3529800-3548800	Weak transcription	Primary T cells from cord blood	blood
10	chr9:3530000-3556400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:3530200-3553600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr9:3531000-3575800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:3531200-3564600	Weak transcription	HSMM	muscle
14	chr9:3531800-3579000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:3532800-3548800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr9:3541800-3542400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:3541800-3553400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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