Variant report

Variant	rs1386930
Chromosome Location	chr3:45884003-45884004
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	MTA3	chr3:45882896-45884096	GM12878	blood:	n/a	n/a
2	CEBPB	chr3:45883257-45884031	MCF-7	breast:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
3	TCF12	chr3:45883168-45884088	ECC-1	luminal epithelium:	n/a	chr3:45883363-45883370
4	MXI1	chr3:45882841-45884011	GM12878	blood:	n/a	n/a
5	SIN3AK20	chr3:45883195-45884049	HCT-116	colon:	n/a	n/a
6	MAX	chr3:45883118-45884158	HCT-116	colon:	n/a	chr3:45883629-45883639
7	MAX	chr3:45883172-45884148	A549	lung:	n/a	chr3:45883629-45883639
8	E2F6	chr3:45883514-45884038	A549	lung:	n/a	n/a
9	E2F6	chr3:45883252-45884142	A549	lung:	n/a	n/a
10	SETDB1	chr3:45883222-45884060	K562	blood:	n/a	n/a
11	GABPA	chr3:45883106-45884267	HL-60	blood:	n/a	chr3:45883710-45883719
12	GABPA	chr3:45883329-45884161	MCF-7	breast:	n/a	chr3:45883710-45883719
13	POLR2A	chr3:45883289-45884027	H1-neurons	neurons:	n/a	n/a
14	CEBPB	chr3:45883309-45884107	ECC-1	luminal epithelium:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
15	MXI1	chr3:45882091-45884476	IMR90	lung:	n/a	n/a
16	CBX3	chr3:45883409-45884028	K562	blood:	n/a	n/a
17	MAX	chr3:45883370-45884126	MCF-7	breast:	n/a	chr3:45883629-45883639
18	GABPA	chr3:45882737-45884433	MCF-7	breast:	n/a	chr3:45883018-45883027 chr3:45883016-45883030 chr3:45883710-45883719
19	RCOR1	chr3:45883374-45884031	GM12878	blood:	n/a	n/a
20	GABPA	chr3:45883082-45884217	SK-N-SH	brain:	n/a	chr3:45883710-45883719
21	GABPA	chr3:45883209-45884156	SK-N-SH	brain:	n/a	chr3:45883710-45883719
22	POLR2A	chr3:45883427-45884022	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr3:45883332-45884040	HCT-116	colon:	n/a	n/a
24	GABPA	chr3:45883419-45884105	HL-60	blood:	n/a	chr3:45883710-45883719
25	POU2F2	chr3:45883330-45884015	GM12891	blood:	n/a	chr3:45883648-45883661 chr3:45883648-45883661 chr3:45883648-45883661
26	POLR2A	chr3:45883164-45884138	PBDE	blood:	n/a	n/a
27	POLR2A	chr3:45883043-45884071	H1-hESC	embryonic stem cell:	n/a	n/a
28	CEBPB	chr3:45883090-45884223	HCT-116	colon:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
29	JUND	chr3:45883102-45884113	SK-N-SH	brain:	n/a	n/a
30	E2F6	chr3:45883291-45884058	Hela-S3	cervix:	n/a	n/a
31	MAX	chr3:45883113-45884173	ECC-1	luminal epithelium:	n/a	chr3:45883629-45883639
32	CEBPB	chr3:45883296-45884052	GM12878	blood:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
33	MAX	chr3:45883198-45884068	H1-hESC	embryonic stem cell:	n/a	chr3:45883629-45883639
34	POLR2A	chr3:45883562-45884039	U87	brain:	n/a	n/a
35	ATF2	chr3:45883375-45884048	GM12878	blood:	n/a	n/a
36	MAX	chr3:45883128-45884198	HepG2	liver:	n/a	chr3:45883629-45883639
37	POLR2A	chr3:45883277-45884123	U87	brain:	n/a	n/a
38	GABPA	chr3:45883337-45884103	K562	blood:	n/a	chr3:45883710-45883719
39	MTA3	chr3:45883064-45884020	GM12878	blood:	n/a	n/a
40	CEBPB	chr3:45883040-45884185	HCT-116	colon:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
41	POLR2A	chr3:45883525-45884079	ECC-1	luminal epithelium:	n/a	n/a
42	YY1	chr3:45883273-45884004	GM12878	blood:	n/a	chr3:45883430-45883444
43	GABPA	chr3:45883202-45884114	A549	lung:	n/a	chr3:45883710-45883719
44	MAX	chr3:45883269-45884099	SK-N-SH	brain:	n/a	chr3:45883629-45883639
45	YY1	chr3:45883381-45884047	GM12878	blood:	n/a	chr3:45883430-45883444
46	POLR2A	chr3:45883488-45884058	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:45883379-45884014	GM18505	blood:	n/a	n/a
48	POLR2A	chr3:45883399-45884021	Hela-S3	cervix:	n/a	n/a
49	TAF1	chr3:45883364-45884015	ECC-1	luminal epithelium:	n/a	n/a
50	IRF4	chr3:45883372-45884019	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LZTFL1	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11130077	0.82[GIH][hapmap];0.87[LWK][hapmap];0.82[YRI][hapmap]
rs1125823	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11712469	1.00[ASN][1000 genomes]
rs11916880	0.81[CHB][hapmap]
rs13065964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1488369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064061	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2129880	0.98[ASN][1000 genomes]
rs7614952	0.86[CHB][hapmap]
rs7625839	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs952287	0.86[CHB][hapmap]
rs9855780	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1386930	DALRD3	cis	cerebellum	SCAN
rs1386930	IP6K1	cis	cerebellum	SCAN
rs1386930	RNF123	cis	cerebellum	SCAN
rs1386930	CDC25A	cis	cerebellum	SCAN
rs1386930	CCDC71	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45882200-45884200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr3:45882200-45886600	Strong transcription	Dnd41	blood
3	chr3:45882400-45884200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr3:45882400-45884400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr3:45882600-45884200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:45882600-45884200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:45882600-45884200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr3:45882600-45884200	Active TSS	Right Atrium	heart
9	chr3:45882600-45884200	Active TSS	A549	lung
10	chr3:45882600-45884200	Active TSS	HSMM	muscle
11	chr3:45882600-45884400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr3:45882800-45884200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr3:45882800-45884200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr3:45882800-45884200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:45882800-45884200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:45882800-45884200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr3:45882800-45884200	Active TSS	Colonic Mucosa	Colon
18	chr3:45882800-45884200	Active TSS	Fetal Intestine Small	intestine
19	chr3:45882800-45884200	Active TSS	Fetal Kidney	kidney
20	chr3:45882800-45884200	Active TSS	Psoas Muscle	Psoas
21	chr3:45882800-45884200	Active TSS	Rectal Smooth Muscle	rectum
22	chr3:45882800-45884200	Active TSS	Right Ventricle	heart
23	chr3:45882800-45884200	Active TSS	Stomach Smooth Muscle	stomach
24	chr3:45882800-45884400	Active TSS	Stomach Mucosa	stomach
25	chr3:45882800-45884600	Active TSS	Duodenum Mucosa	Duodenum
26	chr3:45883000-45884200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:45883000-45884200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:45883000-45884200	Active TSS	Aorta	Aorta
29	chr3:45883000-45884200	Active TSS	Brain Cingulate Gyrus	brain
30	chr3:45883000-45884200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:45883000-45884200	Active TSS	Placenta Amnion	Placenta Amnion
32	chr3:45883000-45884200	Active TSS	HSMMtube	muscle
33	chr3:45883000-45884200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr3:45883000-45884200	Active TSS	NHEK	skin
35	chr3:45883000-45884400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:45883200-45884200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
37	chr3:45883200-45884200	Active TSS	Brain Substantia Nigra	brain
38	chr3:45883200-45884200	Active TSS	Fetal Brain Female	brain
39	chr3:45883800-45884200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:45883800-45884200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr3:45883800-45884200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr3:45883800-45884200	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr3:45883800-45884200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:45883800-45884200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr3:45883800-45884200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:45883800-45884200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr3:45883800-45884200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr3:45883800-45884200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:45883800-45884200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr3:45883800-45884200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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