Variant report

Variant	rs540420
Chromosome Location	chr3:119358977-119358978
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	TCF12	chr3:119358323-119359353	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:119358613-119359270	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr3:119356390-119359464	SK-N-SH	brain:	n/a	chr3:119357125-119357135 chr3:119357061-119357071
4	NFIC	chr3:119356328-119359285	GM12878	blood:	n/a	n/a
5	NFIC	chr3:119358399-119359231	SK-N-SH	brain:	n/a	n/a
6	EP300	chr3:119358318-119359242	SK-N-SH	brain:	n/a	chr3:119358549-119358558
7	RAD21	chr3:119358868-119359157	SK-N-SH_RA	brain:	n/a	n/a
8	GATA3	chr3:119357621-119359298	SH-SY5Y	brain:	n/a	n/a
9	EP300	chr3:119355708-119359660	SK-N-SH	brain:	n/a	chr3:119358021-119358035 chr3:119358549-119358558 chr3:119357930-119357938 chr3:119356957-119356971 chr3:119356958-119356972
10	EP300	chr3:119358518-119359245	SK-N-SH_RA	brain:	n/a	chr3:119358549-119358558
11	TCF12	chr3:119356402-119359447	SK-N-SH	brain:	n/a	chr3:119357774-119357782
12	E2F4	chr3:119358753-119359127	MCF10A-Er-Src	breast:	n/a	n/a
13	MXI1	chr3:119356499-119359364	SK-N-SH	brain:	n/a	n/a
14	EP300	chr3:119358647-119359227	SK-N-SH_RA	brain:	n/a	n/a
15	PML	chr3:119356256-119359119	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:119358874-119359169	SK-N-SH	brain:	n/a	n/a
17	JUND	chr3:119358312-119359237	SK-N-SH	brain:	n/a	chr3:119358550-119358558 chr3:119358549-119358558 chr3:119358575-119358587 chr3:119358551-119358558
18	JUND	chr3:119356288-119359356	SK-N-SH	brain:	n/a	chr3:119358550-119358558 chr3:119358549-119358558 chr3:119358575-119358587 chr3:119358551-119358558
19	GATA3	chr3:119356512-119359281	SK-N-SH	brain:	n/a	chr3:119357125-119357135 chr3:119357061-119357071
20	CEBPB	chr3:119356654-119358982	GM12878	blood:	n/a	chr3:119357855-119357866 chr3:119357854-119357867
21	GATA2	chr3:119357518-119359232	SH-SY5Y	brain:	n/a	n/a
22	PBX3	chr3:119358372-119359220	SK-N-SH	brain:	n/a	n/a
23	FOXM1	chr3:119356553-119359017	GM12878	blood:	n/a	chr3:119358106-119358114

Variant related genes	Relation type
ENSG00000242052	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11914676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923223	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12487499	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488460	0.94[ASN][1000 genomes]
rs12490779	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12492456	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065893	0.81[JPT][hapmap]
rs1403631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525836	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830115	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830291	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17203235	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1797827	0.97[ASN][1000 genomes]
rs1872432	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1985121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280578	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2629409	0.81[JPT][hapmap]
rs2670292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688629	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688630	0.97[ASN][1000 genomes]
rs2688631	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688634	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692616	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698283	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34097211	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34593263	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34787881	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35043554	0.94[ASN][1000 genomes]
rs35256565	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3749416	0.81[JPT][hapmap]
rs4234662	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629367	0.87[ASN][1000 genomes]
rs4687869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688024	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484809	0.85[JPT][hapmap]
rs523476	0.81[JPT][hapmap]
rs524043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552244	0.81[JPT][hapmap]
rs571352	0.85[JPT][hapmap]
rs572119	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579196	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766563	0.89[CHB][hapmap]
rs67683909	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789941	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790938	0.86[ASN][1000 genomes]
rs6792417	0.87[ASN][1000 genomes]
rs6794579	0.89[JPT][hapmap]
rs6803814	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs68150601	0.87[ASN][1000 genomes]
rs71325388	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71325389	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613825	0.94[ASN][1000 genomes]
rs7626940	0.89[CHB][hapmap]
rs7633444	0.80[JPT][hapmap]
rs8422	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876919	0.95[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv1796433	chr3:119350324-119360506	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1804126	chr3:119351398-119360506	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv527724	chr3:119353844-119361415	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	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
rs540420	COX17	Cis_1M	lymphoblastoid	RTeQTL
rs540420	POPDC2	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119341400-119364600	Weak transcription	Liver	Liver
2	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
4	chr3:119352600-119367000	Weak transcription	Ovary	ovary
5	chr3:119353800-119359000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:119354800-119360400	Weak transcription	Lung	lung
8	chr3:119355400-119361000	Weak transcription	Pancreas	Pancrea
9	chr3:119356200-119360200	Weak transcription	Primary T cells from cord blood	blood
10	chr3:119356200-119360800	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:119356800-119360800	Weak transcription	Aorta	Aorta
13	chr3:119356800-119361400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:119356800-119364800	Weak transcription	Stomach Mucosa	stomach
15	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
17	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:119357200-119359200	Enhancers	NHDF-Ad	bronchial
19	chr3:119357200-119361800	Weak transcription	A549	lung
20	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
21	chr3:119357800-119359000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:119357800-119359000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr3:119357800-119360000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:119357800-119360200	Weak transcription	Psoas Muscle	Psoas
25	chr3:119357800-119360600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:119357800-119360800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:119357800-119360800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:119357800-119361800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:119357800-119366600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr3:119357800-119367000	Weak transcription	Fetal Intestine Large	intestine
31	chr3:119357800-119386400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:119358000-119360200	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:119358000-119360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:119358000-119360400	Weak transcription	Fetal Stomach	stomach
35	chr3:119358000-119360800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:119358000-119360800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:119358000-119361000	Weak transcription	Right Ventricle	heart
38	chr3:119358000-119361000	Weak transcription	Spleen	Spleen
39	chr3:119358000-119361800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:119358000-119361800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:119358000-119361800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:119358000-119361800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:119358000-119361800	Weak transcription	NH-A	brain
44	chr3:119358000-119362000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:119358000-119362000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:119358000-119371200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
48	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
49	chr3:119358200-119359400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:119358200-119361200	Weak transcription	NHLF	lung

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