Variant report

Variant	rs4296215
Chromosome Location	chr15:82560819-82560820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11073036	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11630197	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11631813	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][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]
rs11633000	0.85[ASN][1000 genomes]
rs11639440	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11854289	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11854483	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12324875	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1501367	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1566559	0.81[ASN][1000 genomes]
rs1566560	0.81[ASN][1000 genomes]
rs1566561	0.95[ASN][1000 genomes]
rs16973457	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1846908	0.81[ASN][1000 genomes]
rs1948741	0.92[ASN][1000 genomes]
rs1948742	0.93[CHB][hapmap];0.91[ASN][1000 genomes]
rs1972460	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2016372	0.96[ASN][1000 genomes]
rs2047679	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2134046	0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2457497	0.93[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2665103	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs28454949	0.86[ASN][1000 genomes]
rs28522807	0.89[ASN][1000 genomes]
rs3759800	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3858953	0.87[ASN][1000 genomes]
rs3902959	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4238534	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4267268	0.94[ASN][1000 genomes]
rs4778674	0.87[ASN][1000 genomes]
rs4778986	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs4778987	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs4778990	0.87[ASN][1000 genomes]
rs56398167	0.92[ASN][1000 genomes]
rs61554133	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7167504	0.93[ASN][1000 genomes]
rs7176926	0.83[ASN][1000 genomes]
rs72749540	0.92[ASN][1000 genomes]
rs72749557	0.93[ASN][1000 genomes]
rs72749560	0.93[ASN][1000 genomes]
rs72749561	0.93[ASN][1000 genomes]
rs72749564	0.94[ASN][1000 genomes]
rs72749575	0.90[ASN][1000 genomes]
rs72749586	0.96[ASN][1000 genomes]
rs7403041	0.87[ASN][1000 genomes]
rs7403244	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8025964	0.90[ASN][1000 genomes]
rs8027301	0.93[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs8027661	0.93[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs8030210	0.92[ASN][1000 genomes]
rs8030250	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs8032633	0.92[ASN][1000 genomes]
rs8033313	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs905450	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs9972440	0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4296215	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82555400-82565400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:82555800-82561200	Weak transcription	Fetal Thymus	thymus
3	chr15:82555800-82566400	Weak transcription	Ovary	ovary
4	chr15:82556000-82561000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:82556000-82561200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:82556000-82561400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:82556000-82561600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:82556000-82563200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:82556000-82566400	Weak transcription	Fetal Lung	lung
10	chr15:82556200-82567400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:82558400-82561000	Enhancers	Primary B cells from cord blood	blood
12	chr15:82558600-82561800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr15:82558600-82562000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:82558600-82562000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:82558600-82562200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr15:82558800-82561200	Enhancers	NHEK	skin
17	chr15:82558800-82562000	Enhancers	Primary T cells from cord blood	blood
18	chr15:82559600-82561200	Enhancers	HMEC	breast
19	chr15:82559600-82564000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:82559600-82567400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr15:82559800-82561200	Enhancers	K562	blood
22	chr15:82560200-82561400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:82560200-82561800	Enhancers	Thymus	Thymus
24	chr15:82560400-82561200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:82560400-82561200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:82560400-82561400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:82560600-82561000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:82560600-82561000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:82560600-82561000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:82560600-82561000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:82560600-82561600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr15:82560600-82562000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:82560800-82561000	Enhancers	Fetal Heart	heart
34	chr15:82560800-82561200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:82560800-82561400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:82560800-82561400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:82560800-82561800	Enhancers	GM12878-XiMat	blood

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