Variant report

Variant	rs27125
Chromosome Location	chr5:115637755-115637756
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-4	chr5:115637354-115638100	NONHSAT103359

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10042177	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs10051072	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap]
rs10051302	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10056823	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10063312	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs10066081	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap]
rs10073458	0.83[EUR][1000 genomes]
rs10075063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs10077013	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs10078121	0.91[CHB][hapmap]
rs10079176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs10079466	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs10079691	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1090077	0.88[EUR][1000 genomes]
rs1090078	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11241372	0.83[EUR][1000 genomes]
rs11241374	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs11241375	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs11742938	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11953135	0.83[EUR][1000 genomes]
rs12054994	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap]
rs12109104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12657249	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs13159102	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap]
rs13161146	0.83[EUR][1000 genomes]
rs13161987	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs13162293	0.82[EUR][1000 genomes]
rs13172482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs1382343	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1382344	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1396478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs1396481	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs1396482	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs149131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1508875	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap]
rs153588	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs153593	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153594	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567335	0.87[CEU][hapmap];0.91[MEX][hapmap]
rs1644268	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1669136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1677405	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1677406	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1677415	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs173813	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs173834	0.87[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs185263	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs253950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs253951	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs253952	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs253955	0.82[AMR][1000 genomes]
rs253959	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs253961	0.81[ASN][1000 genomes]
rs254150	0.86[CHB][hapmap]
rs254151	0.91[CHB][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs254152	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs254171	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs254172	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs254173	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs254174	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs27126	0.88[ASN][1000 genomes]
rs27368	0.82[ASN][1000 genomes]
rs28031	0.82[ASN][1000 genomes]
rs37180	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40192	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41271	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42959	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4921063	1.00[YRI][hapmap]
rs55783029	0.83[EUR][1000 genomes]
rs6594948	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6594952	0.90[YRI][hapmap]
rs6861437	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712561	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs712574	0.84[ASN][1000 genomes]
rs712579	0.84[ASN][1000 genomes]
rs712588	0.84[ASN][1000 genomes]
rs712591	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712592	0.84[ASN][1000 genomes]
rs712593	0.84[ASN][1000 genomes]
rs712594	0.84[ASN][1000 genomes]
rs712595	0.84[ASN][1000 genomes]
rs712596	0.84[ASN][1000 genomes]
rs712597	0.84[ASN][1000 genomes]
rs712598	0.84[ASN][1000 genomes]
rs712599	0.84[ASN][1000 genomes]
rs712600	0.84[ASN][1000 genomes]
rs712601	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7723358	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7732346	0.82[EUR][1000 genomes]
rs7735539	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs784479	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs784481	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs785367	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs785369	0.84[ASN][1000 genomes]
rs785370	0.84[ASN][1000 genomes]
rs785373	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785374	0.84[ASN][1000 genomes]
rs785375	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs785377	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs803967	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs809188	0.88[EUR][1000 genomes]
rs809210	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs810742	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	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
5	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
6	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
7	nsv869754	chr5:115634234-115696094	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs27125	COMMD10	cis	multi-tissue	Pritchard
rs27125	COMMD10	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115613400-115641600	Weak transcription	HSMM	muscle
2	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
3	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
5	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:115627800-115639200	Weak transcription	Placenta	Placenta
7	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:115628400-115639200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:115628400-115641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:115628600-115639400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
13	chr5:115629400-115638200	Weak transcription	Pancreas	Pancrea
14	chr5:115629400-115638400	Weak transcription	Right Ventricle	heart
15	chr5:115631400-115637800	Weak transcription	Fetal Thymus	thymus
16	chr5:115631800-115640600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:115631800-115641800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:115632000-115639200	Weak transcription	Lung	lung
19	chr5:115632000-115643000	Weak transcription	NH-A	brain
20	chr5:115632600-115640400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:115632600-115640600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:115632600-115643400	Weak transcription	Stomach Mucosa	stomach
23	chr5:115632800-115639600	Weak transcription	Brain Angular Gyrus	brain
24	chr5:115632800-115642600	Weak transcription	NHDF-Ad	bronchial
25	chr5:115633200-115640800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:115633600-115639800	Weak transcription	Spleen	Spleen
27	chr5:115633800-115638200	Weak transcription	HSMMtube	muscle
28	chr5:115633800-115640400	Weak transcription	Esophagus	oesophagus
29	chr5:115634000-115637800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:115634000-115640400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:115634200-115639000	Weak transcription	Small Intestine	intestine
32	chr5:115634200-115639200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:115634200-115639200	Weak transcription	Colonic Mucosa	Colon
34	chr5:115634200-115639200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:115634200-115639400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:115634200-115639400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:115634200-115639600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:115634200-115639600	Weak transcription	Dnd41	blood
39	chr5:115634200-115640200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:115634200-115640400	Weak transcription	Fetal Intestine Small	intestine
41	chr5:115634200-115640600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:115634200-115640600	Weak transcription	Thymus	Thymus
43	chr5:115634200-115640800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:115634200-115640800	Weak transcription	Psoas Muscle	Psoas
45	chr5:115634200-115641400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr5:115634200-115641800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:115634200-115641800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr5:115634200-115642200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:115634200-115643600	Weak transcription	HepG2	liver
50	chr5:115634200-115664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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