Variant report

Variant	rs7711510
Chromosome Location	chr5:115632253-115632254
allele	A/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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-4	chr5:115632111-115632653	NONHSAT103359

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10035646	0.85[CEU][hapmap]
rs10036292	0.85[CEU][hapmap]
rs10040345	0.85[CEU][hapmap]
rs10042278	0.85[CEU][hapmap]
rs10043228	0.85[CEU][hapmap]
rs10051240	0.85[CEU][hapmap]
rs10051697	0.85[CEU][hapmap]
rs10054989	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10057462	0.80[JPT][hapmap]
rs10059989	0.80[JPT][hapmap]
rs10062588	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs10066259	0.82[CEU][hapmap]
rs10068730	0.80[JPT][hapmap]
rs10069565	0.86[JPT][hapmap]
rs10071359	0.80[JPT][hapmap]
rs10074746	0.80[JPT][hapmap]
rs10076543	0.80[JPT][hapmap]
rs10077113	0.80[JPT][hapmap]
rs10155600	0.82[CEU][hapmap]
rs10478277	0.85[CEU][hapmap]
rs10478278	0.85[CEU][hapmap]
rs10478281	0.85[CEU][hapmap]
rs10519448	0.85[CEU][hapmap]
rs10519454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10519455	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12152996	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12153717	0.85[CEU][hapmap]
rs12514600	1.00[CEU][hapmap]
rs12516100	0.85[CEU][hapmap]
rs12518094	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12519989	0.85[CEU][hapmap]
rs12520568	0.85[CEU][hapmap]
rs12520613	0.85[CEU][hapmap]
rs12521345	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12521815	0.85[CEU][hapmap]
rs12522441	0.85[CEU][hapmap]
rs12523347	0.85[CEU][hapmap]
rs13362043	0.85[CEU][hapmap]
rs1508870	0.80[JPT][hapmap]
rs1581024	0.82[CEU][hapmap]
rs1582430	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17138907	0.85[CEU][hapmap]
rs17138917	0.85[CEU][hapmap]
rs17138925	0.89[CHB][hapmap]
rs17139182	0.89[CHB][hapmap]
rs17139192	0.85[CEU][hapmap]
rs17139193	0.85[CEU][hapmap]
rs17139224	0.85[CEU][hapmap]
rs17139265	0.85[CEU][hapmap]
rs17139366	0.89[CHB][hapmap]
rs17139457	0.85[CEU][hapmap]
rs1876674	0.85[CEU][hapmap]
rs2068456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2136208	0.85[CEU][hapmap]
rs2136214	0.89[CHB][hapmap]
rs2161321	0.86[JPT][hapmap]
rs4260709	0.84[JPT][hapmap]
rs4301260	0.80[JPT][hapmap]
rs4532392	0.85[CEU][hapmap]
rs57434520	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62384471	0.84[AFR][1000 genomes]
rs62384474	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384478	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62384495	0.90[EUR][1000 genomes]
rs6866938	0.81[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6873096	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6873950	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879075	0.85[JPT][hapmap]
rs6880880	1.00[CEU][hapmap]
rs7707191	0.80[JPT][hapmap]
rs7720518	0.80[JPT][hapmap]
rs7721593	0.84[ASN][1000 genomes]
rs7723648	0.93[JPT][hapmap]
rs7727882	0.85[CEU][hapmap]
rs7730943	0.80[JPT][hapmap]
rs7734614	0.80[JPT][hapmap]
rs9326989	0.85[CEU][hapmap]
rs9326990	0.85[CEU][hapmap]
rs9326997	0.80[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7711510	COMMD10	Cis_1M	lymphoblastoid	RTeQTL
rs7711510	COMMD10	cis	Muscle Skeletal	GTEx

Chromatin state (count:80 , 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	chr5:115613600-115633000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:115624400-115633200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:115624400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:115625600-115633200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:115625600-115633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:115625600-115633200	Weak transcription	Psoas Muscle	Psoas
10	chr5:115625600-115633600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:115625600-115633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:115625600-115634000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
14	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:115626000-115633200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:115626000-115633200	Weak transcription	Left Ventricle	heart
17	chr5:115626400-115633400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:115626400-115633800	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:115626600-115633600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
21	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:115627000-115633400	Weak transcription	Fetal Lung	lung
23	chr5:115627000-115633800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:115627200-115635200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:115627400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:115627800-115633200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:115627800-115639200	Weak transcription	Placenta	Placenta
28	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:115628400-115633400	Weak transcription	Fetal Kidney	kidney
30	chr5:115628400-115639200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:115628400-115641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:115628600-115633000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr5:115628600-115633200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:115628600-115633200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr5:115628600-115633400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:115628600-115639400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:115628800-115632600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:115628800-115633600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:115629000-115633200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
42	chr5:115629400-115638200	Weak transcription	Pancreas	Pancrea
43	chr5:115629400-115638400	Weak transcription	Right Ventricle	heart
44	chr5:115629600-115633000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:115629800-115633200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:115630000-115633600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr5:115630600-115633400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr5:115630800-115633600	Weak transcription	Esophagus	oesophagus
49	chr5:115630800-115633600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:115630800-115634000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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