Variant report

Variant	rs7173280
Chromosome Location	chr15:31341364-31341365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10162731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035705	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs1035706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10400821	0.81[JPT][hapmap]
rs10851487	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs11070764	0.85[ASN][1000 genomes]
rs11070767	0.80[CEU][hapmap];0.84[ASN][1000 genomes]
rs11636071	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11636121	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs16955797	0.90[JPT][hapmap]
rs1991214	0.83[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2278133	0.83[CHD][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs2288241	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2288242	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2338834	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2338835	0.85[ASN][1000 genomes]
rs2911849	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2911850	0.85[ASN][1000 genomes]
rs2911851	0.83[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2911853	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2911854	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2959041	1.00[ASN][1000 genomes]
rs2959042	1.00[ASN][1000 genomes]
rs3743234	0.83[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4779501	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4779808	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4779810	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4779811	0.81[ASN][1000 genomes]
rs4779812	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4779813	0.84[ASN][1000 genomes]
rs7165995	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173932	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7174338	1.00[ASN][1000 genomes]
rs7174872	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7179304	0.96[ASN][1000 genomes]
rs8037421	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8041204	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9806389	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
10	nsv903835	chr15:31312743-31384797	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv903836	chr15:31330280-31512652	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7173280	FAN1	cis	cerebellum	SCAN
rs7173280	SNORD115-7	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31326800-31342800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:31339400-31342000	Weak transcription	Stomach Mucosa	stomach
3	chr15:31339400-31344600	Enhancers	Primary B cells from peripheral blood	blood
4	chr15:31340000-31341800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:31340400-31346400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:31340600-31342800	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:31340800-31343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:31340800-31344000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:31341000-31344400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr15:31341200-31341600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:31341200-31341800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:31341200-31341800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:31341200-31342000	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr15:31341200-31342400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr15:31341200-31342800	Enhancers	GM12878-XiMat	blood
16	chr15:31341200-31343400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr15:31341200-31343600	Enhancers	Spleen	Spleen
18	chr15:31341200-31344400	Enhancers	Primary neutrophils fromperipheralblood	blood

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