Variant report

Variant	rs2063249
Chromosome Location	chr5:115415657-115415658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:115415545-115415845	HCT-116	colon:	n/a	n/a
2	POLR2A	chr5:115413885-115416313	K562	blood:	n/a	n/a
3	POLR2A	chr5:115415541-115415741	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:115415546-115416149	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:115413293..115416934-chr5:115419212..115422160,5	MCF-7	breast:
2	chr5:115409968..115416849-chr5:115417165..115422986,15	K562	blood:
3	chr5:115412238..115416929-chr5:115418524..115421820,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272265	TF binding region
ENSG00000271918	Chromatin interaction
ENSG00000145781	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10036669	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10043670	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10059455	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10065178	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10065554	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10068479	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10075063	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10075195	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10079176	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10079903	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10463453	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10463676	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11241352	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11241359	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1129494	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1133187	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11738674	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11738775	0.86[EUR][1000 genomes]
rs11746600	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11950936	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11952043	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11958648	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12656463	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13157583	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13162238	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13172482	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13179593	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13182605	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13184073	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1396478	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1396479	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1508882	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1588267	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2063250	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2221676	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2416426	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2416427	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4383750	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4921062	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4921063	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6594938	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6865237	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6871968	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6876901	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6879929	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6886944	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6889212	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6894046	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6896479	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7703164	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7715797	0.81[AMR][1000 genomes]
rs7730551	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7734295	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9326986	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9326987	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv515611	chr5:115208843-115428381	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1021968	chr5:115213162-115426468	Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1024008	chr5:115222974-115431050	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1027117	chr5:115222974-115442883	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763487	chr5:115222986-115442895	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv462400	chr5:115223504-115428381	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv599478	chr5:115223504-115428381	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv1030480	chr5:115228889-115446861	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv599479	chr5:115233116-115450969	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv1015976	chr5:115236239-115434163	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv537868	chr5:115236239-115434163	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv882736	chr5:115254723-115552945	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv882737	chr5:115263853-115552945	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	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
17	nsv527320	chr5:115382097-115573543	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv1027266	chr5:115382704-115501792	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
19	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
20	nsv1032199	chr5:115384131-115525738	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
21	esv2830404	chr5:115386661-115490546	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	nsv1019972	chr5:115386860-115563533	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
23	nsv537869	chr5:115386860-115563533	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
24	nsv1018861	chr5:115397834-115563533	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
25	nsv537870	chr5:115397834-115563533	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2063249	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115405400-115419600	Weak transcription	Fetal Brain Male	brain
2	chr5:115410600-115419400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:115411000-115419600	Weak transcription	Fetal Intestine Small	intestine
4	chr5:115411000-115419600	Weak transcription	Pancreas	Pancrea
5	chr5:115411400-115419600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:115411600-115419400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:115411600-115419400	Weak transcription	K562	blood
8	chr5:115411600-115419600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:115412600-115419600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:115412800-115419800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:115413000-115419400	Weak transcription	Primary B cells from cord blood	blood
12	chr5:115413000-115419600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:115413000-115419600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:115413000-115419800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:115413200-115419600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:115413200-115419600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr5:115413200-115419600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:115413200-115419800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr5:115413400-115419400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:115413400-115419600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr5:115413400-115419600	Weak transcription	Left Ventricle	heart
22	chr5:115413400-115420000	Weak transcription	Aorta	Aorta
23	chr5:115413600-115419600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:115414000-115415800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr5:115414000-115416000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:115414000-115416800	Strong transcription	Fetal Stomach	stomach
27	chr5:115414000-115419600	Weak transcription	Primary T cells from cord blood	blood
28	chr5:115414200-115419400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr5:115414200-115419600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:115414600-115419600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:115414600-115419600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:115414600-115419800	Weak transcription	Brain Germinal Matrix	brain
33	chr5:115414800-115419400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:115414800-115419800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:115415000-115419600	Weak transcription	Brain Hippocampus Middle	brain
36	chr5:115415400-115419600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:115415600-115415800	Enhancers	Right Ventricle	heart
38	chr5:115415600-115416200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr5:115415600-115416400	Strong transcription	Fetal Muscle Leg	muscle
40	chr5:115415600-115416800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:115415600-115419600	Weak transcription	Lung	lung

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