Variant report

Variant	rs6866938
Chromosome Location	chr5:115628117-115628118
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10054989	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10062588	0.86[JPT][hapmap]
rs10155600	0.81[AMR][1000 genomes]
rs10519454	0.82[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10519455	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12152996	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12518094	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521345	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1582430	0.86[EUR][1000 genomes]
rs17139224	0.80[MEX][hapmap]
rs17139366	0.82[CHD][hapmap]
rs17139455	0.85[CHD][hapmap]
rs17139457	0.86[MEX][hapmap]
rs1876674	0.86[MEX][hapmap]
rs2068456	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]
rs4466201	0.81[MEX][hapmap]
rs4593303	0.87[MEX][hapmap]
rs57434520	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62384469	0.81[AMR][1000 genomes]
rs62384471	0.83[AFR][1000 genomes]
rs62384474	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62384478	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62384495	0.87[EUR][1000 genomes]
rs6873096	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873950	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711510	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7721593	0.82[ASN][1000 genomes]
rs7723648	0.85[JPT][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6866938	COMMD10	Cis_1M	lymphoblastoid	RTeQTL
rs6866938	COMMD10	cis	multi-tissue	Pritchard
rs6866938	MYH6	trans	parietal	SCAN
rs6866938	COMMD10	cis	Muscle Skeletal	GTEx
rs6866938	COMMD10	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 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	chr5:115624400-115631800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:115624400-115633200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:115624400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:115624600-115628200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:115625600-115632200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:115625600-115633200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:115625600-115633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:115625600-115633200	Weak transcription	Psoas Muscle	Psoas
16	chr5:115625600-115633600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:115625600-115633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:115625600-115634000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
20	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:115625800-115630800	Weak transcription	Fetal Intestine Large	intestine
22	chr5:115625800-115631000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:115626000-115633200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:115626000-115633200	Weak transcription	Left Ventricle	heart
25	chr5:115626200-115632000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:115626400-115628400	Enhancers	Fetal Kidney	kidney
27	chr5:115626400-115633400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:115626400-115633800	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:115626600-115633600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
31	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:115627000-115629400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr5:115627000-115632000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr5:115627000-115633400	Weak transcription	Fetal Lung	lung
35	chr5:115627000-115633800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:115627200-115632200	Weak transcription	Adipose Nuclei	Adipose
37	chr5:115627200-115635200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:115627400-115628800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr5:115627400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:115627600-115630200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:115627800-115628400	Strong transcription	Primary T cells from cord blood	blood
42	chr5:115627800-115628600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr5:115627800-115628600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr5:115627800-115628600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:115627800-115629600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:115627800-115629800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr5:115627800-115630000	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr5:115627800-115630000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr5:115627800-115633200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:115627800-115639200	Weak transcription	Placenta	Placenta

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