Variant report

Variant	rs253951
Chromosome Location	chr5:115633010-115633011
allele	A/G
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:
2	chr5:115630950..115633524-chr5:115633964..115636710,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10056823	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10063312	0.81[EUR][1000 genomes]
rs10063392	0.81[EUR][1000 genomes]
rs10073458	0.82[EUR][1000 genomes]
rs1090077	0.87[EUR][1000 genomes]
rs1090078	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11241372	0.82[EUR][1000 genomes]
rs11241374	0.81[EUR][1000 genomes]
rs11241375	0.81[EUR][1000 genomes]
rs11953135	0.82[EUR][1000 genomes]
rs11960815	0.82[EUR][1000 genomes]
rs12109104	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12657249	0.81[EUR][1000 genomes]
rs13161146	0.82[EUR][1000 genomes]
rs13161987	0.82[EUR][1000 genomes]
rs13162293	0.81[EUR][1000 genomes]
rs1382343	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1382344	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs149131	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153588	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs153593	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1644268	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669135	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669136	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1677405	0.86[EUR][1000 genomes]
rs1677406	0.82[AMR][1000 genomes];0.93[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	0.85[ASN][1000 genomes]
rs185263	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs253950	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253952	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253955	0.80[AMR][1000 genomes]
rs253959	0.84[EUR][1000 genomes]
rs254151	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs254152	0.83[ASN][1000 genomes]
rs254171	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs254172	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs254173	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs254174	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27125	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.98[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	0.82[EUR][1000 genomes]
rs6861437	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712561	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];0.94[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];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7723358	0.84[EUR][1000 genomes]
rs7732346	0.82[EUR][1000 genomes]
rs784479	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	0.83[ASN][1000 genomes]
rs785369	0.83[ASN][1000 genomes]
rs785370	0.83[ASN][1000 genomes]
rs785373	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs785374	0.83[ASN][1000 genomes]
rs785375	0.92[AMR][1000 genomes];0.92[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	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs809188	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs809210	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs810742	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs253951	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 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	chr5:115624400-115633200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:115624400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:115625600-115633200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:115625600-115633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:115625600-115633200	Weak transcription	Psoas Muscle	Psoas
9	chr5:115625600-115633600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:115625600-115633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:115625600-115634000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
13	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:115626000-115633200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:115626000-115633200	Weak transcription	Left Ventricle	heart
16	chr5:115626400-115633400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:115626400-115633800	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:115626600-115633600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
20	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:115627000-115633400	Weak transcription	Fetal Lung	lung
22	chr5:115627000-115633800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:115627200-115635200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:115627400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:115627800-115633200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr5:115627800-115639200	Weak transcription	Placenta	Placenta
27	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:115628400-115633400	Weak transcription	Fetal Kidney	kidney
29	chr5:115628400-115639200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:115628400-115641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:115628600-115633200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:115628600-115633200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:115628600-115633400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:115628600-115639400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:115628800-115633600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:115629000-115633200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
39	chr5:115629400-115638200	Weak transcription	Pancreas	Pancrea
40	chr5:115629400-115638400	Weak transcription	Right Ventricle	heart
41	chr5:115629800-115633200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:115630000-115633600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr5:115630600-115633400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:115630800-115633600	Weak transcription	Esophagus	oesophagus
45	chr5:115630800-115633600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:115630800-115634000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr5:115631200-115633200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr5:115631400-115633200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:115631400-115633200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:115631400-115636200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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