Variant report

Variant	rs1013292
Chromosome Location	chr2:37864141-37864142
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37859378..37862018-chr2:37863759..37867582,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-QPCT-3	chr2:37832379-37870742	NONHSAT070127

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1013291	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10694	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12622958	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs13387842	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13392288	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13406302	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13417833	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13417957	0.94[ASN][1000 genomes]
rs1468663	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1468664	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17021174	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2041508	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072419	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2079998	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2098198	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2109821	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2109822	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2159726	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2191841	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2373290	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2373292	0.87[ASN][1000 genomes]
rs3731852	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3731854	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4372883	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4594425	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4670210	0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs4670745	0.81[AMR][1000 genomes]
rs4670748	0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs6544095	0.87[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs6711909	0.91[CHB][hapmap]
rs6740127	0.82[ASN][1000 genomes]
rs6752119	0.91[CHB][hapmap]
rs6752220	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6752762	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6759224	0.81[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs7607934	0.82[JPT][hapmap];0.87[MEX][hapmap]
rs7735	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9742	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456374	chr2:37669487-37868214	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv470453	chr2:37669487-37868214	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv581473	chr2:37669487-37868214	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1013292	CDC42EP3	cis	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37873200	Weak transcription	Liver	Liver
2	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
3	chr2:37857000-37871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:37857200-37865200	Weak transcription	Left Ventricle	heart
5	chr2:37857200-37865800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:37857200-37868200	Weak transcription	Psoas Muscle	Psoas
7	chr2:37858000-37868600	Weak transcription	A549	lung
8	chr2:37858400-37867600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:37858800-37871400	Weak transcription	Aorta	Aorta
10	chr2:37859000-37868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:37859200-37868600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:37859600-37865000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:37859800-37864200	Weak transcription	Fetal Heart	heart
14	chr2:37860000-37871200	Weak transcription	Gastric	stomach
15	chr2:37860200-37864800	Enhancers	Primary hematopoietic stem cells	blood
16	chr2:37860200-37864800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:37860200-37866800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr2:37860200-37868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:37860400-37864800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:37860400-37865600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr2:37860400-37865600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:37860400-37867400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:37860800-37867000	Weak transcription	NHLF	lung
24	chr2:37860800-37873000	Weak transcription	Pancreas	Pancrea
25	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:37861000-37864600	Enhancers	Primary B cells from peripheral blood	blood
27	chr2:37861000-37865600	Enhancers	Fetal Thymus	thymus
28	chr2:37861000-37868000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:37861200-37864600	Enhancers	Primary T cells from cord blood	blood
30	chr2:37861800-37864200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:37861800-37864200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr2:37861800-37864200	Enhancers	Spleen	Spleen
33	chr2:37861800-37866200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:37862000-37864400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:37862000-37865600	Enhancers	Thymus	Thymus
36	chr2:37862000-37866600	Enhancers	HSMM	muscle
37	chr2:37862000-37867000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:37862000-37869400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:37862200-37864400	Enhancers	Adipose Nuclei	Adipose
40	chr2:37862200-37865600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:37862200-37866800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:37862200-37867000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr2:37862200-37867200	Enhancers	NHDF-Ad	bronchial
44	chr2:37862200-37870600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:37862400-37864200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:37862400-37864400	Enhancers	GM12878-XiMat	blood
47	chr2:37862400-37864800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr2:37862400-37869200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:37862400-37870200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:37862600-37865000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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