Variant report

Variant	rs10065069
Chromosome Location	chr5:49951537-49951538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:49951146..49952897-chr5:49957210..49959408,2	MCF-7	breast:
2	chr5:49949575..49951807-chr5:49954503..49956971,2	MCF-7	breast:
3	chr5:49951519..49954288-chr5:49991653..49994102,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271752	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10038842	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10039639	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs10043477	0.97[AMR][1000 genomes]
rs10070517	0.97[AMR][1000 genomes]
rs10434558	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10471940	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10471956	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10755235	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs10940497	1.00[CEU][hapmap]
rs11739828	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11750771	1.00[CEU][hapmap]
rs12188262	1.00[CEU][hapmap]
rs12188654	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12518710	1.00[JPT][hapmap]
rs13153982	0.81[EUR][1000 genomes]
rs13164951	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes]
rs1375127	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs154137	1.00[CEU][hapmap]
rs154138	1.00[CEU][hapmap]
rs157970	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16884018	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs169497	0.91[CEU][hapmap]
rs171555	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs182230	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1839128	0.91[CEU][hapmap]
rs1988613	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2354526	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2548581	1.00[CEU][hapmap]
rs2548582	0.81[CEU][hapmap]
rs256340	1.00[CEU][hapmap]
rs256341	1.00[CEU][hapmap]
rs26062	0.92[CEU][hapmap]
rs26065	1.00[CEU][hapmap]
rs26068	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs26069	1.00[CEU][hapmap]
rs26071	1.00[CEU][hapmap]
rs2697662	1.00[CEU][hapmap];0.97[AMR][1000 genomes]
rs27245	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs27251	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs27467	1.00[CEU][hapmap]
rs27468	1.00[CEU][hapmap]
rs27469	1.00[CEU][hapmap]
rs27627	1.00[CEU][hapmap]
rs282549	0.82[AMR][1000 genomes]
rs282550	1.00[CEU][hapmap]
rs282552	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs282553	1.00[CEU][hapmap]
rs282559	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs282561	1.00[CEU][hapmap]
rs32404	0.86[CEU][hapmap]
rs32425	1.00[CEU][hapmap]
rs3763367	0.82[EUR][1000 genomes]
rs39613	1.00[CEU][hapmap]
rs4029420	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs42284	1.00[CEU][hapmap]
rs4865628	1.00[CEU][hapmap]
rs4865974	1.00[JPT][hapmap]
rs4866001	1.00[JPT][hapmap]
rs57079776	0.87[EUR][1000 genomes]
rs578198	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs62366937	0.82[EUR][1000 genomes]
rs6450301	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6450359	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6869356	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6872496	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6886872	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6890519	1.00[CEU][hapmap]
rs6890869	1.00[CEU][hapmap]
rs7449019	0.92[AMR][1000 genomes]
rs7711839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7723361	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7734389	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs895801	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs921210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes]

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	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv964851	chr5:49945480-49952101	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10065069	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs10065069	PARP8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49949200-49951800	Enhancers	Primary B cells from cord blood	blood
2	chr5:49949400-49951600	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr5:49949600-49952800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr5:49949800-49961600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:49950000-49952000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:49950000-49959400	Weak transcription	Primary T cells from cord blood	blood
7	chr5:49950200-49951600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:49950200-49951800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr5:49950200-49952000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr5:49950200-49952200	Weak transcription	Small Intestine	intestine
11	chr5:49950200-49959200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:49950800-49951600	Enhancers	Dnd41	blood
13	chr5:49951000-49953200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:49951200-49953400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr5:49951200-49954000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:49951400-49951600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:49951400-49952000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:49951400-49952600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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