Variant report

Variant	rs9742
Chromosome Location	chr2:37869494-37869495
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1013291	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1013292	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10694	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11883958	0.82[ASN][1000 genomes]
rs12622958	0.86[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs13387842	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13392288	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13406302	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13417833	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13417957	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1468663	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1468664	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17021174	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2041508	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2072419	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2079998	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2098198	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2109821	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2109822	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2159726	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2191841	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2373290	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2373292	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3731852	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372883	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4594425	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4670210	0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs4670211	0.81[ASN][1000 genomes]
rs4670745	0.84[AMR][1000 genomes]
rs4670748	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[ASN][1000 genomes]
rs56809883	0.81[ASN][1000 genomes]
rs6544095	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs6711909	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs6722589	0.83[ASN][1000 genomes]
rs6740127	0.87[ASN][1000 genomes]
rs6752119	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs6752220	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6752762	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6759224	0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs7607934	0.82[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs7735	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9742	CDC42EP3	cis	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

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	chr2:37858800-37871400	Weak transcription	Aorta	Aorta
5	chr2:37860000-37871200	Weak transcription	Gastric	stomach
6	chr2:37860800-37873000	Weak transcription	Pancreas	Pancrea
7	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:37862200-37870600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:37862400-37870200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:37863400-37875000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:37863600-37871400	Weak transcription	Lung	lung
12	chr2:37863600-37873000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:37864200-37870200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:37864200-37871200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:37864200-37871200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:37864200-37871400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:37864200-37871400	Weak transcription	Spleen	Spleen
18	chr2:37864200-37880200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:37864400-37870600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:37864400-37871400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:37864400-37871400	Weak transcription	Adipose Nuclei	Adipose
22	chr2:37864400-37872000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:37864400-37879400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:37864600-37870200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:37864600-37871000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:37864800-37870200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:37865000-37869800	Weak transcription	Primary B cells from cord blood	blood
28	chr2:37865400-37869800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:37865600-37873000	Weak transcription	Ovary	ovary
30	chr2:37866400-37871400	Weak transcription	Brain Germinal Matrix	brain
31	chr2:37866600-37875200	Genic enhancers	HSMM	muscle
32	chr2:37866800-37870000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:37866800-37875000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:37866800-37881000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:37867000-37870200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:37867000-37880600	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr2:37867200-37875000	Genic enhancers	NHDF-Ad	bronchial
38	chr2:37867400-37870200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:37867400-37872800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:37867400-37874800	Weak transcription	Fetal Intestine Small	intestine
41	chr2:37867600-37871200	Weak transcription	Placenta	Placenta
42	chr2:37867800-37871400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:37868000-37870200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:37868000-37870200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr2:37868000-37872800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:37868000-37873600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:37868000-37875200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:37868000-37876200	Genic enhancers	Osteobl	bone
49	chr2:37868200-37869600	Enhancers	Fetal Muscle Leg	muscle
50	chr2:37868200-37869600	Enhancers	Right Atrium	heart

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