Variant report

Variant	rs2068456
Chromosome Location	chr5:115627570-115627571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

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	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10062588	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs10066259	0.82[CEU][hapmap]
rs10069565	0.85[JPT][hapmap]
rs10073199	0.81[CHD][hapmap]
rs10155600	0.82[CEU][hapmap]
rs10478277	0.85[CEU][hapmap]
rs10478278	0.85[CEU][hapmap]
rs10478281	0.85[CEU][hapmap]
rs10478286	0.80[CHD][hapmap]
rs10478287	0.80[CHD][hapmap]
rs10519448	0.85[CEU][hapmap]
rs10519454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10519455	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11957382	0.81[CHD][hapmap]
rs12152996	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12153717	0.85[CEU][hapmap]
rs12514600	1.00[CEU][hapmap]
rs12516100	0.85[CEU][hapmap]
rs12518094	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519989	0.85[CEU][hapmap]
rs12520568	0.85[CEU][hapmap];0.93[MEX][hapmap]
rs12520613	0.85[CEU][hapmap]
rs12521345	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12521815	0.85[CEU][hapmap]
rs12522441	0.85[CEU][hapmap]
rs12523347	0.85[CEU][hapmap]
rs13362043	0.85[CEU][hapmap]
rs1396484	0.80[CHD][hapmap]
rs1396486	0.81[CHD][hapmap]
rs1508873	0.80[CHD][hapmap]
rs1567339	0.80[CHD][hapmap]
rs1581024	0.82[CEU][hapmap]
rs1582430	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17138907	0.85[CEU][hapmap]
rs17138917	0.85[CEU][hapmap]
rs17139192	0.85[CEU][hapmap]
rs17139193	0.85[CEU][hapmap]
rs17139224	0.85[CEU][hapmap];0.93[MEX][hapmap]
rs17139265	0.85[CEU][hapmap];0.85[MEX][hapmap]
rs17139366	0.82[CHD][hapmap]
rs17139455	0.85[CHD][hapmap]
rs17139457	0.85[CEU][hapmap];0.85[MEX][hapmap]
rs1876672	0.81[CHD][hapmap]
rs1876674	0.85[CEU][hapmap];0.85[MEX][hapmap]
rs2136208	0.85[CEU][hapmap]
rs2161321	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2174996	0.81[CHD][hapmap]
rs2416434	0.80[CHD][hapmap]
rs4260709	0.82[JPT][hapmap]
rs4466201	0.81[MEX][hapmap]
rs4484468	0.81[CHD][hapmap]
rs4532392	0.85[CEU][hapmap]
rs4593303	0.80[CHD][hapmap];0.86[MEX][hapmap]
rs4921078	0.80[CHD][hapmap]
rs57434520	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62384474	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62384478	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62384495	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6866938	0.82[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873096	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873950	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6878871	0.81[CHD][hapmap]
rs6879075	0.85[JPT][hapmap]
rs6880880	1.00[CEU][hapmap]
rs6887275	0.80[CHD][hapmap]
rs6887852	0.81[CHD][hapmap]
rs7711510	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7718843	0.81[CHD][hapmap]
rs7721593	0.82[ASN][1000 genomes]
rs7723648	0.92[JPT][hapmap]
rs7727882	0.85[CEU][hapmap]
rs9326989	0.85[CEU][hapmap]
rs9326990	0.85[CEU][hapmap]
rs9686231	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	esv2760969	chr5:115583627-115630890	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	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
12	nsv1020633	chr5:115596277-115629523	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1023495	chr5:115596277-115629769	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	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
15	nsv1018649	chr5:115596350-115629523	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1015300	chr5:115597953-115629523	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1028664	chr5:115601522-115630878	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1034438	chr5:115612225-115630878	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2068456	COMMD10	cis	lymphoblastoid	seeQTL
rs2068456	COMMD10	Cis_1M	lymphoblastoid	RTeQTL
rs2068456	COMMD10	cis	Muscle Skeletal	GTEx

Chromatin state (count:56 , 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	chr5:115613400-115628200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:115613400-115641600	Weak transcription	HSMM	muscle
5	chr5:115613600-115632000	Weak transcription	Fetal Heart	heart
6	chr5:115613600-115633000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:115624200-115631800	Weak transcription	Liver	Liver
8	chr5:115624400-115627800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:115624400-115631800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:115624400-115633200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:115624400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:115624600-115627600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:115624600-115627800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr5:115624600-115627800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:115624600-115628200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:115624800-115628000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:115624800-115628000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:115625000-115628000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:115625400-115627800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:115625600-115628000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr5:115625600-115628000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr5:115625600-115632200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:115625600-115633200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr5:115625600-115633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:115625600-115633200	Weak transcription	Psoas Muscle	Psoas
26	chr5:115625600-115633600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:115625600-115633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:115625600-115634000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
30	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:115625800-115628000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr5:115625800-115630800	Weak transcription	Fetal Intestine Large	intestine
33	chr5:115625800-115631000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr5:115626000-115633200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:115626000-115633200	Weak transcription	Left Ventricle	heart
36	chr5:115626200-115632000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:115626400-115627800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:115626400-115628000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:115626400-115628400	Enhancers	Fetal Kidney	kidney
40	chr5:115626400-115633400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:115626400-115633800	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:115626600-115627800	Weak transcription	Primary T cells from cord blood	blood
43	chr5:115626600-115633600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
45	chr5:115626800-115628000	Weak transcription	Primary B cells from cord blood	blood
46	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr5:115627000-115629400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr5:115627000-115632000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr5:115627000-115633400	Weak transcription	Fetal Lung	lung
50	chr5:115627000-115633800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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