Variant report

Variant	rs253952
Chromosome Location	chr5:115633670-115633671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115632385..115634405-chr5:115635053..115637473,2	K562	blood:

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10042177	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10051072	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10051302	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs10056823	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10063312	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs10063392	0.82[EUR][1000 genomes]
rs10066081	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10073458	0.83[EUR][1000 genomes]
rs10075063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10077013	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10078121	0.91[CHB][hapmap]
rs10079176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10079466	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10079691	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1090077	0.88[EUR][1000 genomes]
rs1090078	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11241372	0.83[EUR][1000 genomes]
rs11241374	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs11241375	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs11742938	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11953135	0.83[EUR][1000 genomes]
rs11960815	0.83[EUR][1000 genomes]
rs12054994	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12109104	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12657249	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs13159102	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13161146	0.83[EUR][1000 genomes]
rs13161987	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs13162293	0.82[EUR][1000 genomes]
rs13172482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1382343	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1382344	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1396478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1396481	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1396482	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs149131	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1508875	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs153588	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs153593	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153594	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1567335	0.87[CEU][hapmap]
rs1588267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1644268	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1677405	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1677406	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1677415	0.80[ASN][1000 genomes]
rs173813	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs173834	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs185263	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs253950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253951	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253955	0.80[AMR][1000 genomes]
rs253959	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs254150	0.83[CHB][hapmap]
rs254151	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs254152	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs254171	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs254172	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs254173	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs254174	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27125	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27126	0.86[ASN][1000 genomes]
rs27368	0.81[ASN][1000 genomes]
rs28031	0.81[ASN][1000 genomes]
rs37180	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40192	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41271	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42959	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55783029	0.83[EUR][1000 genomes]
rs6594948	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6861437	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6871132	0.85[YRI][hapmap]
rs712561	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs712574	0.83[ASN][1000 genomes]
rs712579	0.83[ASN][1000 genomes]
rs712588	0.83[ASN][1000 genomes]
rs712591	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712592	0.83[ASN][1000 genomes]
rs712593	0.83[ASN][1000 genomes]
rs712594	0.83[ASN][1000 genomes]
rs712595	0.83[ASN][1000 genomes]
rs712596	0.83[ASN][1000 genomes]
rs712597	0.83[ASN][1000 genomes]
rs712598	0.83[ASN][1000 genomes]
rs712599	0.83[ASN][1000 genomes]
rs712600	0.83[ASN][1000 genomes]
rs712601	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7723358	0.95[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs7732346	0.82[EUR][1000 genomes]
rs7735539	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs784479	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs784481	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs785367	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs785369	0.83[ASN][1000 genomes]
rs785370	0.83[ASN][1000 genomes]
rs785373	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs785374	0.83[ASN][1000 genomes]
rs785375	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs785377	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs803967	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs809188	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs809210	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs810742	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs253952	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115613400-115641600	Weak transcription	HSMM	muscle
2	chr5:115625600-115633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:115625600-115634000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
5	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:115626400-115633800	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
8	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:115627000-115633800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:115627200-115635200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:115627800-115639200	Weak transcription	Placenta	Placenta
12	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:115628400-115639200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:115628400-115641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:115628600-115639400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
18	chr5:115629400-115638200	Weak transcription	Pancreas	Pancrea
19	chr5:115629400-115638400	Weak transcription	Right Ventricle	heart
20	chr5:115630800-115634000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:115631400-115636200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:115631400-115637800	Weak transcription	Fetal Thymus	thymus
23	chr5:115631800-115640600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:115631800-115641800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr5:115632000-115634200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
26	chr5:115632000-115634800	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr5:115632000-115639200	Weak transcription	Lung	lung
28	chr5:115632000-115643000	Weak transcription	NH-A	brain
29	chr5:115632200-115634000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
30	chr5:115632200-115634600	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr5:115632200-115635600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:115632400-115634200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
33	chr5:115632600-115634600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
34	chr5:115632600-115640400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:115632600-115640600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:115632600-115643400	Weak transcription	Stomach Mucosa	stomach
37	chr5:115632800-115633800	Weak transcription	Brain Anterior Caudate	brain
38	chr5:115632800-115639600	Weak transcription	Brain Angular Gyrus	brain
39	chr5:115632800-115642600	Weak transcription	NHDF-Ad	bronchial
40	chr5:115633000-115633800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:115633000-115634200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:115633000-115634600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr5:115633000-115634600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
44	chr5:115633000-115635800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:115633200-115634000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:115633200-115634000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:115633200-115634200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
48	chr5:115633200-115634200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
49	chr5:115633200-115634200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr5:115633200-115634200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--

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