Variant report

Variant	rs11920853
Chromosome Location	chr3:47308183-47308184
allele	A/G/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	MAX	chr3:47308126-47308609	K562	blood:	n/a	chr3:47308379-47308388 chr3:47308378-47308387
2	JUND	chr3:47308071-47308755	HCT-116	colon:	n/a	chr3:47308377-47308388 chr3:47308379-47308387 chr3:47308378-47308388 chr3:47308380-47308387 chr3:47308375-47308386
3	ATF3	chr3:47308145-47308653	K562	blood:	n/a	n/a
4	ATF2	chr3:47308168-47308523	GM12878	blood:	n/a	n/a
5	RCOR1	chr3:47308157-47308842	K562	blood:	n/a	n/a
6	POLR2A	chr3:47308169-47308674	K562	blood:	n/a	n/a
7	FOSL1	chr3:47308159-47308767	K562	blood:	n/a	chr3:47308379-47308387 chr3:47308378-47308388 chr3:47308380-47308387 chr3:47308377-47308388 chr3:47308375-47308386
8	SPI1	chr3:47308170-47308581	K562	blood:	n/a	n/a
9	SPI1	chr3:47308124-47308396	GM12891	blood:	n/a	n/a
10	MAX	chr3:47308165-47308421	Hela-S3	cervix:	n/a	chr3:47308379-47308388 chr3:47308378-47308387
11	FOXM1	chr3:47308167-47308589	GM12878	blood:	n/a	n/a
12	FOSL2	chr3:47308118-47308608	HepG2	liver:	n/a	chr3:47308379-47308387 chr3:47308378-47308388 chr3:47308380-47308387 chr3:47308375-47308386 chr3:47308376-47308387
13	POLR2A	chr3:47308169-47308500	SK-N-SH	brain:	n/a	n/a
14	SPI1	chr3:47308039-47308671	HL-60	blood:	n/a	n/a
15	MTA3	chr3:47308065-47308679	GM12878	blood:	n/a	n/a
16	MXI1	chr3:47308014-47309147	SK-N-SH	brain:	n/a	n/a
17	PML	chr3:47308066-47308725	GM12878	blood:	n/a	n/a
18	FOSL2	chr3:47308123-47308519	HepG2	liver:	n/a	chr3:47308379-47308387 chr3:47308378-47308388 chr3:47308380-47308387 chr3:47308375-47308386 chr3:47308376-47308387
19	UBTF	chr3:47308179-47308697	K562	blood:	n/a	n/a
20	NFIC	chr3:47308116-47308786	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:47308180-47308706	HL-60	blood:	n/a	n/a
22	EGR1	chr3:47308166-47308756	K562	blood:	n/a	n/a
23	RUNX3	chr3:47308023-47308729	GM12878	blood:	n/a	n/a
24	NR2F2	chr3:47307932-47308774	K562	blood:	n/a	n/a
25	FOS	chr3:47308129-47308669	HUVEC	blood vessel:	n/a	chr3:47308377-47308388 chr3:47308379-47308387 chr3:47308378-47308388 chr3:47308380-47308387 chr3:47308375-47308386
26	EGR1	chr3:47308085-47308422	K562	blood:	n/a	n/a
27	SPI1	chr3:47308181-47308563	K562	blood:	n/a	n/a
28	NFIC	chr3:47308177-47308704	SK-N-SH	brain:	n/a	n/a
29	MAX	chr3:47308151-47308574	NB4	blood:	n/a	chr3:47308379-47308388 chr3:47308378-47308387
30	TCF3	chr3:47308147-47308474	GM12878	blood:	n/a	n/a
31	NFIC	chr3:47308125-47308750	ECC-1	luminal epithelium:	n/a	n/a
32	PML	chr3:47308090-47308663	K562	blood:	n/a	n/a
33	TRIM28	chr3:47308085-47308876	K562	blood:	n/a	n/a
34	NFIC	chr3:47308136-47308662	SK-N-SH	brain:	n/a	n/a
35	USF1	chr3:47308125-47308520	K562	blood:	n/a	n/a
36	TEAD4	chr3:47307962-47308906	K562	blood:	n/a	n/a
37	TCF12	chr3:47308056-47308757	SK-N-SH	brain:	n/a	n/a
38	MYC	chr3:47308150-47308504	MCF10A-Er-Src	breast:	n/a	chr3:47308379-47308388 chr3:47308378-47308387
39	JUN	chr3:47307945-47309326	K562	blood:	n/a	chr3:47308379-47308387 chr3:47308378-47308388 chr3:47308380-47308387 chr3:47308375-47308386
40	CBX3	chr3:47308036-47308805	K562	blood:	n/a	n/a
41	NFIC	chr3:47308147-47308678	ECC-1	luminal epithelium:	n/a	n/a
42	FOSL2	chr3:47308102-47308626	SK-N-SH	brain:	n/a	chr3:47308379-47308387 chr3:47308378-47308388 chr3:47308380-47308387 chr3:47308375-47308386 chr3:47308376-47308387
43	RUNX3	chr3:47308149-47308742	GM12878	blood:	n/a	n/a
44	ATF2	chr3:47308130-47308651	GM12878	blood:	n/a	n/a
45	TEAD4	chr3:47308057-47308847	K562	blood:	n/a	n/a
46	CEBPB	chr3:47308139-47308589	K562	blood:	n/a	n/a
47	JUND	chr3:47307990-47308776	SK-N-SH	brain:	n/a	chr3:47308377-47308388 chr3:47308379-47308387 chr3:47308378-47308388 chr3:47308380-47308387 chr3:47308375-47308386
48	MYC	chr3:47308145-47308667	NB4	blood:	n/a	chr3:47308379-47308388 chr3:47308378-47308387
49	TCF12	chr3:47308026-47308784	SK-N-SH	brain:	n/a	n/a
50	MEF2A	chr3:47308126-47308709	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47306715..47308916-chr3:47322571..47324674,2	MCF-7	breast:

Variant related genes	Relation type
KIF9	TF binding region
ENSG00000114648	Chromatin interaction
ENSG00000088727	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1038394	0.88[CEU][hapmap]
rs10490798	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1076394	0.92[CEU][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs10865946	0.89[CEU][hapmap]
rs11130115	0.82[CEU][hapmap]
rs11130123	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs11130124	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11130126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11130128	0.89[CEU][hapmap]
rs11130129	0.88[CEU][hapmap]
rs11705957	0.88[CEU][hapmap]
rs11710013	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs11710121	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11710322	0.92[CEU][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs11711824	0.88[CEU][hapmap]
rs11712445	0.92[CEU][hapmap]
rs11714294	0.85[EUR][1000 genomes]
rs11719877	0.88[CEU][hapmap]
rs11720439	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11915074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11920354	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11921117	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11925560	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12631730	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12636851	0.88[CEU][hapmap]
rs13061071	0.82[CEU][hapmap]
rs13075233	0.88[CEU][hapmap]
rs13094438	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1466740	0.89[AFR][1000 genomes]
rs1466741	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1531875	0.88[CEU][hapmap]
rs1638676	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs17410853	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17411375	0.92[CEU][hapmap]
rs17476234	0.87[EUR][1000 genomes]
rs1872164	0.88[CEU][hapmap]
rs2088135	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2101247	0.84[CEU][hapmap]
rs2132173	0.81[CEU][hapmap]
rs2159400	0.92[CEU][hapmap]
rs2240796	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2276853	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2276854	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs295428	0.92[CEU][hapmap]
rs295441	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs295442	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs295449	0.92[CEU][hapmap]
rs295458	0.92[CEU][hapmap]
rs295461	0.92[CEU][hapmap]
rs3736177	0.88[CEU][hapmap]
rs4682852	0.83[CEU][hapmap]
rs4683326	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4858811	0.89[CEU][hapmap]
rs4858824	0.89[CEU][hapmap]
rs4858868	0.88[CEU][hapmap]
rs4858893	0.89[CEU][hapmap]
rs4858894	0.84[CEU][hapmap]
rs56250009	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57756484	0.82[AFR][1000 genomes]
rs58472056	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61386020	0.85[ASN][1000 genomes]
rs62246455	0.82[AFR][1000 genomes]
rs62248905	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6767907	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs6768221	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6772670	0.92[CEU][hapmap]
rs6773521	0.82[AFR][1000 genomes]
rs6780013	0.96[CEU][hapmap]
rs6781941	0.82[AFR][1000 genomes]
rs6791842	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs6792461	0.88[CEU][hapmap]
rs6800271	0.88[CEU][hapmap]
rs73069104	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7433300	0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7620997	0.81[AFR][1000 genomes]
rs7632501	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636423	0.90[EUR][1000 genomes]
rs7651762	0.88[CEU][hapmap]
rs807932	0.88[CEU][hapmap]
rs807935	0.85[EUR][1000 genomes]
rs807936	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs807937	0.86[EUR][1000 genomes]
rs811115	0.87[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs878659	0.88[CEU][hapmap]
rs922957	0.89[CEU][hapmap]
rs9311403	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap]
rs9683033	0.88[CEU][hapmap]
rs9837343	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]

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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11920853	DHX30	cis	multi-tissue	Pritchard
rs11920853	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11920853	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47264200-47322200	Weak transcription	Gastric	stomach
2	chr3:47282800-47322400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:47285400-47315800	Weak transcription	Pancreas	Pancrea
4	chr3:47285600-47312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:47293600-47323200	Weak transcription	Spleen	Spleen
6	chr3:47299400-47308200	Weak transcription	Right Atrium	heart
7	chr3:47300800-47322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:47301000-47322800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:47301200-47323000	Weak transcription	Psoas Muscle	Psoas
10	chr3:47302600-47314600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:47302600-47322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:47302800-47323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:47303200-47308400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:47305600-47323200	Weak transcription	Primary T cells from cord blood	blood
15	chr3:47305800-47315000	Weak transcription	Fetal Intestine Small	intestine
16	chr3:47306000-47308400	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:47306600-47308200	Enhancers	K562	blood
18	chr3:47306600-47309000	Enhancers	Fetal Muscle Leg	muscle
19	chr3:47306600-47309000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:47306600-47309000	Enhancers	GM12878-XiMat	blood
21	chr3:47306800-47309000	Enhancers	HSMM	muscle
22	chr3:47306800-47309200	Enhancers	HSMMtube	muscle
23	chr3:47306800-47310000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:47307000-47308800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:47307000-47309000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:47307000-47314800	Weak transcription	Lung	lung
27	chr3:47307200-47308200	Weak transcription	Brain Anterior Caudate	brain
28	chr3:47307200-47308800	Enhancers	Brain Substantia Nigra	brain
29	chr3:47307200-47308800	Enhancers	HMEC	breast
30	chr3:47307200-47309000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:47307200-47309000	Enhancers	NH-A	brain
32	chr3:47307200-47309200	Enhancers	Fetal Heart	heart
33	chr3:47307200-47309200	Enhancers	NHLF	lung
34	chr3:47307200-47309800	Enhancers	Dnd41	blood
35	chr3:47307200-47310800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:47307400-47308800	Enhancers	HepG2	liver
37	chr3:47307600-47308800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:47307600-47308800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:47307600-47309000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:47307800-47308200	Enhancers	Right Ventricle	heart
41	chr3:47307800-47308800	Enhancers	NHDF-Ad	bronchial
42	chr3:47307800-47308800	Enhancers	NHEK	skin
43	chr3:47307800-47309000	Enhancers	Brain Cingulate Gyrus	brain
44	chr3:47307800-47311000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:47308000-47308200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:47308000-47308400	Enhancers	Fetal Stomach	stomach
47	chr3:47308000-47308600	Enhancers	Stomach Mucosa	stomach
48	chr3:47308000-47308800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:47308000-47308800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr3:47308000-47308800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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