Variant report

Variant	rs11854289
Chromosome Location	chr15:82558802-82558803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr15:82558651-82560205	K562	blood:	n/a	n/a
2	EP300	chr15:82558796-82558916	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:82558753-82559033	K562	blood:	n/a	n/a

Variant related genes	Relation type
EFTUD1	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11073036	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11630197	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11631813	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11633000	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11639440	0.94[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs11854483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324875	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1501367	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1566559	0.91[ASN][1000 genomes]
rs1566560	0.91[ASN][1000 genomes]
rs1566561	0.84[ASN][1000 genomes]
rs16973457	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1846908	0.91[ASN][1000 genomes]
rs1948741	0.81[ASN][1000 genomes]
rs1948742	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs1972460	0.87[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2016372	0.85[ASN][1000 genomes]
rs2047679	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2134046	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs2457497	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs2665103	0.93[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs28454949	0.94[ASN][1000 genomes]
rs28522807	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28564699	0.81[ASN][1000 genomes]
rs28610286	0.85[ASN][1000 genomes]
rs3759800	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3902959	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4238534	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4267268	0.83[ASN][1000 genomes]
rs4296215	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4778674	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4778986	0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs4778987	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4778990	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56398167	0.83[ASN][1000 genomes]
rs61554133	0.89[ASN][1000 genomes]
rs62012054	0.80[ASN][1000 genomes]
rs62012055	0.82[ASN][1000 genomes]
rs7167504	0.82[ASN][1000 genomes]
rs7176926	0.93[ASN][1000 genomes]
rs72749540	0.81[ASN][1000 genomes]
rs72749557	0.82[ASN][1000 genomes]
rs72749560	0.82[ASN][1000 genomes]
rs72749561	0.82[ASN][1000 genomes]
rs72749564	0.83[ASN][1000 genomes]
rs72749586	0.85[ASN][1000 genomes]
rs7403041	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7403244	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8025964	0.83[ASN][1000 genomes]
rs8027301	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8027661	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8030210	0.81[ASN][1000 genomes]
rs8030250	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs8032633	0.81[ASN][1000 genomes]
rs8033313	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs905450	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9972440	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv457213	chr15:82456227-82573255	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv570244	chr15:82456227-82573255	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv570246	chr15:82485707-82581264	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1041506	chr15:82496164-82581427	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv1798145	chr15:82506790-82581264	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv904440	chr15:82524544-82591082	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv904441	chr15:82532963-82580736	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv904442	chr15:82540174-82571046	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1054025	chr15:82540486-83058214	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv904443	chr15:82553472-82571780	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11854289	ACSBG1	cis	cerebellum	SCAN
rs11854289	AP3B2	cis	cerebellum	SCAN
rs11854289	FAM154B	cis	cerebellum	SCAN
rs11854289	AP3B2	cis	parietal	SCAN
rs11854289	SH2D7	cis	cerebellum	SCAN
rs11854289	FAM154B	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82555400-82565400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:82555800-82559400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:82555800-82560200	Weak transcription	Thymus	Thymus
4	chr15:82555800-82561200	Weak transcription	Fetal Thymus	thymus
5	chr15:82555800-82566400	Weak transcription	Ovary	ovary
6	chr15:82556000-82559400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:82556000-82559400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:82556000-82559600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:82556000-82559600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:82556000-82559600	Weak transcription	HMEC	breast
11	chr15:82556000-82560800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:82556000-82561000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:82556000-82561200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:82556000-82561400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:82556000-82561600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:82556000-82563200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:82556000-82566400	Weak transcription	Fetal Lung	lung
18	chr15:82556200-82560000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:82556200-82560600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:82556200-82567400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:82556800-82560600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:82558400-82560400	Enhancers	Primary B cells from peripheral blood	blood
23	chr15:82558400-82561000	Enhancers	Primary B cells from cord blood	blood
24	chr15:82558600-82559000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr15:82558600-82559000	Enhancers	K562	blood
26	chr15:82558600-82559400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr15:82558600-82559600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr15:82558600-82559800	Enhancers	HUVEC	blood vessel
29	chr15:82558600-82560200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr15:82558600-82560200	Enhancers	Fetal Heart	heart
31	chr15:82558600-82560400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr15:82558600-82560600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:82558600-82561800	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr15:82558600-82562000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr15:82558600-82562000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr15:82558600-82562200	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr15:82558800-82559200	Flanking Active TSS	GM12878-XiMat	blood
38	chr15:82558800-82559600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:82558800-82559600	Enhancers	Primary hematopoietic stem cells	blood
40	chr15:82558800-82559600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:82558800-82559800	Enhancers	Stomach Mucosa	stomach
42	chr15:82558800-82561200	Enhancers	NHEK	skin
43	chr15:82558800-82562000	Enhancers	Primary T cells from cord blood	blood

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