Variant report

Variant	rs254152
Chromosome Location	chr5:115641827-115641828
allele	C/G
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	CTCF	chr5:115641680-115641830	HepG2	liver:	n/a	chr5:115641778-115641786
2	CTCF	chr5:115641760-115641910	HCPEpiC	choroid plexus:	n/a	chr5:115641778-115641786

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-4	chr5:115641553-115642622	NONHSAT103359

Variant related genes	Relation type
ENSG00000250015	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10042177	0.82[CHB][hapmap]
rs10051072	0.82[CHB][hapmap]
rs10051302	0.82[CHB][hapmap]
rs10063312	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs10066081	0.87[CHB][hapmap]
rs10075063	0.82[CHB][hapmap]
rs10078121	0.91[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap]
rs10079176	0.87[CHB][hapmap]
rs10079466	0.82[CHB][hapmap]
rs10079691	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs1090078	0.84[ASN][1000 genomes]
rs11241374	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs11241375	0.82[CHB][hapmap]
rs11742938	0.82[CHB][hapmap]
rs12054994	0.82[CHB][hapmap]
rs12109104	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs12657249	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs13159102	0.81[CHB][hapmap]
rs13172482	0.82[CHB][hapmap]
rs1382343	0.80[ASN][1000 genomes]
rs1382344	0.80[ASN][1000 genomes]
rs1396478	0.82[CHB][hapmap]
rs1396481	0.82[CHB][hapmap]
rs1396482	0.82[CHB][hapmap]
rs149131	0.86[ASN][1000 genomes]
rs1508875	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs153593	0.86[ASN][1000 genomes]
rs153594	0.86[ASN][1000 genomes]
rs1644268	0.85[ASN][1000 genomes]
rs1669135	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs1669136	0.82[CHB][hapmap]
rs1677406	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs173834	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs185263	0.89[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs253950	0.82[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs253951	0.83[ASN][1000 genomes]
rs253952	0.83[ASN][1000 genomes]
rs253959	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs254150	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs254151	0.91[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs254171	0.86[CHB][hapmap]
rs254172	0.86[CHB][hapmap]
rs254173	0.86[CHB][hapmap]
rs254174	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs27125	0.86[ASN][1000 genomes]
rs27126	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs37180	0.82[ASN][1000 genomes]
rs40192	0.82[ASN][1000 genomes]
rs41271	0.82[ASN][1000 genomes]
rs6594948	0.82[CHB][hapmap]
rs712561	0.82[CHB][hapmap]
rs712574	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712576	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712577	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs712591	0.87[ASN][1000 genomes]
rs712601	0.85[ASN][1000 genomes]
rs7735539	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs784479	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs784480	0.82[CEU][hapmap]
rs784481	0.80[ASN][1000 genomes]
rs785367	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs785369	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs785370	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs785371	0.86[ASN][1000 genomes]
rs785373	0.87[ASN][1000 genomes]
rs785375	0.86[ASN][1000 genomes]
rs785377	0.86[ASN][1000 genomes]
rs803967	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs809210	0.80[ASN][1000 genomes]
rs810742	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	nsv869754	chr5:115634234-115696094	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1018001	chr5:115640603-115660285	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs254152	COMMD10	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
6	chr5:115632000-115643000	Weak transcription	NH-A	brain
7	chr5:115632600-115643400	Weak transcription	Stomach Mucosa	stomach
8	chr5:115632800-115642600	Weak transcription	NHDF-Ad	bronchial
9	chr5:115634200-115642200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:115634200-115643600	Weak transcription	HepG2	liver
11	chr5:115634200-115664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:115634400-115645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:115635400-115642400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr5:115635400-115642600	Strong transcription	Left Ventricle	heart
15	chr5:115635400-115643600	Strong transcription	Fetal Intestine Large	intestine
16	chr5:115636200-115643600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:115637600-115643400	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:115637600-115643800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:115637800-115642400	Enhancers	Liver	Liver
20	chr5:115637800-115642800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:115638200-115642600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:115638200-115642800	Strong transcription	Pancreas	Pancrea
23	chr5:115638400-115643000	Strong transcription	Right Ventricle	heart
24	chr5:115638400-115643400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:115638400-115644000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:115638800-115643400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:115639000-115644400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:115639200-115642000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:115639200-115642000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:115639200-115643200	Strong transcription	Placenta	Placenta
31	chr5:115639400-115642800	Strong transcription	A549	lung
32	chr5:115639400-115643000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:115639400-115645200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
34	chr5:115639600-115642200	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:115639600-115642800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:115639600-115643000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:115639600-115643600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:115639600-115647400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:115639800-115642600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:115639800-115643000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:115639800-115643400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:115640000-115644200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:115640200-115642600	Strong transcription	HSMMtube	muscle
44	chr5:115640200-115643600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr5:115640200-115645600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
46	chr5:115640200-115647200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr5:115640400-115642000	Strong transcription	Brain Hippocampus Middle	brain
48	chr5:115640400-115643000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:115640400-115643000	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr5:115640400-115643200	ZNF genes & repeats	Aorta	Aorta

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