Variant report

Variant	rs515339
Chromosome Location	chr9:97347954-97347955
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	chr9:97315728..97317499-chr9:97347623..97350500,3	MCF-7	breast:
2	chr9:97346870..97349447-chr9:97350199..97352748,2	K562	blood:

Variant related genes	Relation type
ENSG00000231806	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1042144	0.89[EUR][1000 genomes]
rs12238876	0.84[EUR][1000 genomes]
rs13291835	0.85[EUR][1000 genomes]
rs13296485	0.87[EUR][1000 genomes]
rs1754435	0.87[EUR][1000 genomes]
rs1754439	0.89[EUR][1000 genomes]
rs2460138	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2679599	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2679600	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2679602	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2772013	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2772022	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2790390	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2945799	0.88[EUR][1000 genomes]
rs2945802	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2987882	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2987897	0.87[EUR][1000 genomes]
rs2993912	0.85[EUR][1000 genomes]
rs2993958	0.87[EUR][1000 genomes]
rs2993959	0.87[EUR][1000 genomes]
rs2993961	0.87[EUR][1000 genomes]
rs2993962	0.87[EUR][1000 genomes]
rs4075984	0.87[EUR][1000 genomes]
rs479197	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs514222	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs518768	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs540124	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs543731	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs547834	0.86[EUR][1000 genomes]
rs548348	0.89[EUR][1000 genomes]
rs576745	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs583365	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs590090	0.91[AFR][1000 genomes]
rs632506	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs652867	0.92[AFR][1000 genomes]
rs688843	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs693399	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs781650	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs802918	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs802919	0.83[EUR][1000 genomes]
rs8192689	0.86[EUR][1000 genomes]
rs874248	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[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	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases
2	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv466436	chr9:97343620-97369149	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv614917	chr9:97343620-97369149	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97317200-97354000	Weak transcription	Gastric	stomach
2	chr9:97335000-97349600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:97340000-97349000	Weak transcription	Fetal Stomach	stomach
4	chr9:97343800-97348800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr9:97344400-97348800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:97346200-97351600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:97346600-97348000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:97347000-97348200	Enhancers	GM12878-XiMat	blood
9	chr9:97347400-97348800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:97347400-97351200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:97347400-97353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr9:97347600-97374000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:97347800-97348800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr9:97347800-97348800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr9:97347800-97348800	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:97347800-97349000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:97347800-97349200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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