Variant report

Variant	rs62384471
Chromosome Location	chr5:115631273-115631274
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115630950..115633524-chr5:115633964..115636710,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10035646	0.80[EUR][1000 genomes]
rs10036292	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10040345	0.80[EUR][1000 genomes]
rs10042278	0.80[EUR][1000 genomes]
rs10043228	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10051240	0.84[EUR][1000 genomes]
rs10052306	0.80[EUR][1000 genomes]
rs10054248	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10063296	0.80[EUR][1000 genomes]
rs10073364	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10079089	0.80[EUR][1000 genomes]
rs10079394	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10155600	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10519448	0.84[EUR][1000 genomes]
rs12152964	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12153338	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153717	0.84[EUR][1000 genomes]
rs12153778	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332489	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12332585	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12332658	0.84[EUR][1000 genomes]
rs12514110	0.83[ASN][1000 genomes]
rs12515251	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515466	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12519989	0.84[EUR][1000 genomes]
rs12520568	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12520613	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12520632	0.88[EUR][1000 genomes]
rs12521440	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521612	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12522027	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12522441	0.80[EUR][1000 genomes]
rs12523347	0.84[EUR][1000 genomes]
rs13362043	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1382339	0.84[EUR][1000 genomes]
rs1422500	0.84[EUR][1000 genomes]
rs1592917	0.84[EUR][1000 genomes]
rs17139192	0.84[EUR][1000 genomes]
rs17139193	0.84[EUR][1000 genomes]
rs17139224	0.84[EUR][1000 genomes]
rs17139265	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17139314	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17139457	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35696109	0.80[EUR][1000 genomes]
rs4283834	0.80[EUR][1000 genomes]
rs4398671	0.84[EUR][1000 genomes]
rs59447169	0.80[EUR][1000 genomes]
rs62384212	0.80[EUR][1000 genomes]
rs62384213	0.80[EUR][1000 genomes]
rs62384215	0.80[EUR][1000 genomes]
rs62384229	0.80[EUR][1000 genomes]
rs62384230	0.80[EUR][1000 genomes]
rs62384231	0.80[EUR][1000 genomes]
rs62384233	0.80[EUR][1000 genomes]
rs62384235	0.80[EUR][1000 genomes]
rs62384236	0.80[EUR][1000 genomes]
rs62384237	0.84[EUR][1000 genomes]
rs62384238	0.84[EUR][1000 genomes]
rs62384253	0.80[EUR][1000 genomes]
rs62384461	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62384468	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62384469	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384476	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62384477	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62384491	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62385975	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62385980	0.88[EUR][1000 genomes]
rs62385993	0.88[EUR][1000 genomes]
rs6866938	0.83[AFR][1000 genomes]
rs6873950	0.84[AFR][1000 genomes]
rs6876972	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880880	0.84[EUR][1000 genomes]
rs7443669	0.80[EUR][1000 genomes]
rs7711510	0.84[AFR][1000 genomes]
rs7727882	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][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	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv882743	chr5:115501792-115634127	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv882747	chr5:115566636-115662510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2755740	chr5:115576139-115633474	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv2757134	chr5:115578810-115633474	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2759372	chr5:115578810-115633474	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv882748	chr5:115584159-115669950	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2752575	chr5:115596277-115633474	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62384471	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115612800-115633200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:115612800-115633200	Weak transcription	Ovary	ovary
3	chr5:115613400-115641600	Weak transcription	HSMM	muscle
4	chr5:115613600-115632000	Weak transcription	Fetal Heart	heart
5	chr5:115613600-115633000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:115624200-115631800	Weak transcription	Liver	Liver
7	chr5:115624400-115631800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:115624400-115633200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:115624400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:115625600-115632200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:115625600-115633200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr5:115625600-115633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:115625600-115633200	Weak transcription	Psoas Muscle	Psoas
14	chr5:115625600-115633600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:115625600-115633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:115625600-115634000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
18	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:115626000-115633200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:115626000-115633200	Weak transcription	Left Ventricle	heart
21	chr5:115626200-115632000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:115626400-115633400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:115626400-115633800	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:115626600-115633600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
26	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:115627000-115632000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:115627000-115633400	Weak transcription	Fetal Lung	lung
29	chr5:115627000-115633800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:115627200-115632200	Weak transcription	Adipose Nuclei	Adipose
31	chr5:115627200-115635200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:115627400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:115627800-115633200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:115627800-115639200	Weak transcription	Placenta	Placenta
35	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:115628400-115632000	Weak transcription	Primary T cells from cord blood	blood
37	chr5:115628400-115633400	Weak transcription	Fetal Kidney	kidney
38	chr5:115628400-115639200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:115628400-115641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:115628600-115633000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:115628600-115633200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr5:115628600-115633200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr5:115628600-115633400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:115628600-115639400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr5:115628800-115632200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:115628800-115632600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr5:115628800-115633600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:115629000-115633200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel

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