Variant report

Variant	rs1862577
Chromosome Location	chr5:37721865-37721866
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	GATA3	chr5:37720165-37722247	SK-N-SH	brain:	n/a	n/a
2	SMC3	chr5:37721726-37721971	GM12878	blood:	n/a	n/a
3	RCOR1	chr5:37721832-37721904	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr5:37721809-37722009	GM12878	blood:	n/a	n/a
5	PBX3	chr5:37721529-37722222	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr5:37720211-37722217	SK-N-SH	brain:	n/a	chr5:37720416-37720425
7	ATF2	chr5:37721531-37722125	GM12878	blood:	n/a	n/a
8	NFIC	chr5:37721463-37722130	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:37721677-37722014	HUVEC	blood vessel:	n/a	n/a
10	MTA3	chr5:37721621-37722099	GM12878	blood:	n/a	n/a
11	EP300	chr5:37721702-37721972	GM12878	blood:	n/a	n/a
12	BATF	chr5:37721687-37721984	GM12878	blood:	n/a	chr5:37721867-37721878
13	EP300	chr5:37721344-37722040	GM12878	blood:	n/a	n/a
14	POLR2A	chr5:37721503-37722160	HUVEC	blood vessel:	n/a	n/a
15	MTA3	chr5:37721534-37722105	GM12878	blood:	n/a	n/a
16	EGR1	chr5:37721708-37721973	GM12878	blood:	n/a	n/a
17	RUNX3	chr5:37721385-37722157	GM12878	blood:	n/a	n/a
18	EP300	chr5:37721798-37721890	GM12878	blood:	n/a	n/a
19	REST	chr5:37721346-37721870	PFSK-1	brain:	n/a	n/a
20	FOS	chr5:37721616-37722198	HUVEC	blood vessel:	n/a	n/a
21	NFIC	chr5:37721579-37722090	GM12878	blood:	n/a	n/a
22	CEBPB	chr5:37721530-37722136	GM12878	blood:	n/a	n/a
23	CEBPB	chr5:37721689-37722004	IMR90	lung:	n/a	n/a
24	BHLHE40	chr5:37721716-37721940	GM12878	blood:	n/a	n/a
25	IKZF1	chr5:37721698-37721892	GM12878	blood:	n/a	n/a
26	GATA2	chr5:37721572-37722164	HUVEC	blood vessel:	n/a	n/a
27	EP300	chr5:37720198-37722140	SK-N-SH	brain:	n/a	n/a
28	BATF	chr5:37721677-37722017	GM12878	blood:	n/a	chr5:37721867-37721878
29	FOXM1	chr5:37721585-37722112	GM12878	blood:	n/a	n/a
30	JUN	chr5:37721556-37722109	HUVEC	blood vessel:	n/a	n/a
31	CHD2	chr5:37721796-37721923	GM12878	blood:	n/a	n/a
32	NFATC1	chr5:37721549-37722097	GM12878	blood:	n/a	n/a
33	PBX3	chr5:37721520-37722144	SK-N-SH	brain:	n/a	n/a
34	RUNX3	chr5:37721525-37722072	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
WDR70	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10461983	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10461984	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10941361	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11749343	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11749345	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12513493	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12517792	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12519774	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12520294	0.83[ASN][1000 genomes]
rs12521092	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12651803	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12656733	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13154033	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13159969	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13171010	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13182520	0.81[ASN][1000 genomes]
rs13182737	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs13185923	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13187416	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1363925	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2973086	1.00[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4431371	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4869542	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs677084	1.00[YRI][hapmap]
rs6897494	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs781794	1.00[YRI][hapmap]
rs870100	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs9292665	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.84[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	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1862577	OXCT1	cis	parietal	SCAN
rs1862577	RXFP3	cis	cerebellum	SCAN
rs1862577	SLC1A3	cis	parietal	SCAN
rs1862577	GDNF	cis	cerebellum	SCAN
rs1862577	LIFR	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37685200-37743200	Weak transcription	Gastric	stomach
2	chr5:37685600-37727000	Weak transcription	Lung	lung
3	chr5:37688400-37723600	Weak transcription	Placenta	Placenta
4	chr5:37689600-37726000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:37695400-37722600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr5:37696800-37722800	Weak transcription	Psoas Muscle	Psoas
7	chr5:37697000-37743800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:37697400-37722200	Weak transcription	HMEC	breast
9	chr5:37702800-37723400	Weak transcription	Thymus	Thymus
10	chr5:37703600-37722800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr5:37704400-37735400	Weak transcription	Brain Angular Gyrus	brain
12	chr5:37704600-37726800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:37705400-37724400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:37710200-37735400	Weak transcription	Brain Substantia Nigra	brain
15	chr5:37714400-37725600	Enhancers	NHDF-Ad	bronchial
16	chr5:37715000-37724600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:37716200-37722600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:37716400-37734800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:37717600-37722600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:37717600-37737600	Weak transcription	Small Intestine	intestine
21	chr5:37717800-37724400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:37717800-37735200	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:37717800-37735200	Weak transcription	Fetal Brain Male	brain
24	chr5:37717800-37735400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:37717800-37735600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:37717800-37756200	Weak transcription	Right Ventricle	heart
27	chr5:37718200-37722400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:37718200-37722600	Weak transcription	K562	blood
29	chr5:37718200-37727000	Weak transcription	Fetal Brain Female	brain
30	chr5:37718200-37727000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:37718200-37727400	Weak transcription	Brain Germinal Matrix	brain
32	chr5:37718400-37722400	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:37718400-37735400	Weak transcription	Brain Anterior Caudate	brain
34	chr5:37718400-37735400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:37718400-37743200	Weak transcription	Aorta	Aorta
36	chr5:37718400-37745400	Weak transcription	Pancreas	Pancrea
37	chr5:37718400-37755800	Weak transcription	Spleen	Spleen
38	chr5:37718600-37722200	Weak transcription	Fetal Kidney	kidney
39	chr5:37718600-37723400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:37718600-37726800	Weak transcription	Liver	Liver
41	chr5:37718800-37722800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr5:37718800-37722800	Weak transcription	Hela-S3	cervix
43	chr5:37718800-37723000	Weak transcription	Ovary	ovary
44	chr5:37718800-37723000	Weak transcription	A549	lung
45	chr5:37718800-37725800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr5:37718800-37735600	Weak transcription	Colon Smooth Muscle	Colon
47	chr5:37718800-37735600	Weak transcription	Fetal Heart	heart
48	chr5:37719000-37722000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:37719000-37727000	Weak transcription	Fetal Lung	lung
50	chr5:37719200-37727000	Weak transcription	Fetal Intestine Large	intestine

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