Variant report

Variant	rs6752220
Chromosome Location	chr2:37875279-37875280
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	POLR2A	chr2:37867842-37879116	U87	brain:	n/a	n/a
2	POLR2A	chr2:37874880-37875451	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:37873373-37876259	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:37874085-37875367	U87	brain:	n/a	n/a
5	STAT3	chr2:37875203-37875578	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr2:37874506-37876510	GM12892	blood:	n/a	n/a
7	POLR2A	chr2:37874573-37876335	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:37874533-37876327	GM12878	blood:	n/a	n/a
9	NFATC1	chr2:37875186-37876155	GM12878	blood:	n/a	chr2:37875358-37875372
10	POLR2A	chr2:37874946-37875559	GM12891	blood:	n/a	n/a
11	POLR2A	chr2:37875210-37875434	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr2:37874389-37877120	GM12891	blood:	n/a	n/a
13	POLR2A	chr2:37874530-37875283	GM12892	blood:	n/a	n/a
14	POLR2A	chr2:37874623-37876203	GM19193	blood:	n/a	n/a
15	POLR2A	chr2:37875254-37876344	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr2:37874489-37876313	GM12891	blood:	n/a	n/a
17	POLR2A	chr2:37871281-37876143	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:37874425-37878298	GM12891	blood:	n/a	n/a
19	POLR2A	chr2:37872360-37878906	U87	brain:	n/a	n/a
20	POLR2A	chr2:37874392-37876318	GM12892	blood:	n/a	n/a
21	POLR2A	chr2:37874398-37876426	GM12892	blood:	n/a	n/a
22	POLR2A	chr2:37874456-37876500	GM12891	blood:	n/a	n/a
23	POLR2A	chr2:37874016-37875367	U87	brain:	n/a	n/a
24	POU2F2	chr2:37875240-37876116	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
CDC42EP3	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1013291	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1013292	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10694	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.94[ASN][1000 genomes]
rs11124594	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11124595	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11883958	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12622958	0.86[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13387842	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13392288	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13406302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13417833	0.82[AMR][1000 genomes]
rs13417957	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1468663	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1468664	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17021174	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2041508	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2079998	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2098198	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2109821	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2109822	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2159726	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2191841	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2373290	0.90[ASN][1000 genomes]
rs2373292	0.87[AMR][1000 genomes]
rs3731852	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3731854	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4372883	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4594425	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4670210	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670211	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4670748	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56809883	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544095	0.88[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67084656	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6709067	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6709621	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6711909	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs6722589	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6740127	0.94[ASN][1000 genomes]
rs6752119	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs6752762	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759224	0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7607934	0.83[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs7735	0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9742	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]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv535647	chr2:37874563-38014428	Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6752220	CDC42EP3	cis	lymphoblastoid	seeQTL
rs6752220	CDC42EP3	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
2	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:37864200-37880200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:37864400-37879400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:37866800-37881000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:37867000-37880600	Genic enhancers	Muscle Satellite Cultured Cells	--
7	chr2:37868000-37876200	Genic enhancers	Osteobl	bone
8	chr2:37868200-37876200	Genic enhancers	NH-A	brain
9	chr2:37868600-37875400	Weak transcription	Fetal Intestine Large	intestine
10	chr2:37868600-37879800	Genic enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:37869400-37876200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:37869800-37875600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
13	chr2:37870000-37875400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr2:37870200-37875400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:37870800-37878600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:37871200-37875800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr2:37871400-37875600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:37871400-37880600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:37871800-37875400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:37872000-37892400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:37872200-37875400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:37872200-37881800	Weak transcription	Fetal Kidney	kidney
23	chr2:37872400-37880800	Weak transcription	Fetal Brain Male	brain
24	chr2:37873000-37875600	Strong transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:37873000-37875600	Genic enhancers	Right Ventricle	heart
26	chr2:37873000-37881400	Enhancers	Right Atrium	heart
27	chr2:37873200-37875400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:37873200-37876200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:37873200-37877200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:37873400-37875400	Weak transcription	Placenta	Placenta
31	chr2:37873400-37876200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:37873400-37876800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr2:37873600-37875400	Weak transcription	Aorta	Aorta
34	chr2:37873600-37875400	Strong transcription	A549	lung
35	chr2:37873600-37876800	Weak transcription	Pancreas	Pancrea
36	chr2:37873600-37879600	Weak transcription	Gastric	stomach
37	chr2:37873600-37879600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:37873600-37880200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:37873600-37881000	Weak transcription	Ovary	ovary
40	chr2:37873800-37875600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
41	chr2:37873800-37889000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr2:37874000-37875400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:37874000-37876000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:37874000-37876200	ZNF genes & repeats	GM12878-XiMat	blood
45	chr2:37874200-37875400	Genic enhancers	Primary B cells from cord blood	blood
46	chr2:37874200-37875600	Genic enhancers	HSMMtube	muscle
47	chr2:37874200-37875800	Enhancers	Brain Hippocampus Middle	brain
48	chr2:37874200-37881600	Genic enhancers	NHLF	lung
49	chr2:37874400-37875600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:37874400-37875800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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