Variant report

Variant	rs2094652
Chromosome Location	chr20:13764654-13764655
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	POLR2A	chr20:13764523-13764708	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr20:13764615-13766484	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr20:13764294-13765893	A549	lung:	n/a	chr20:13765548-13765557
4	JUN	chr20:13764383-13765938	K562	blood:	n/a	n/a
5	MXI1	chr20:13764592-13767089	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:13764475..13767391-chr20:13770944..13774600,4	K562	blood:
2	chr20:13762040..13764842-chr20:13764954..13766584,2	MCF-7	breast:
3	chr20:13618822..13620677-chr20:13764351..13767218,2	MCF-7	breast:

Variant related genes	Relation type
NDUFAF5	TF binding region
ENSG00000089123	Chromatin interaction
ENSG00000089048	Chromatin interaction
ENSG00000101247	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2327796	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2423754	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs243917	1.00[EUR][1000 genomes]
rs34901599	1.00[AMR][1000 genomes]
rs4239710	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814255	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814257	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814259	0.90[AFR][1000 genomes]
rs6033822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042326	0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042334	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042344	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6074639	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6079175	0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6109967	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active 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	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2094652	LOC728606	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13749000-13765200	Weak transcription	Small Intestine	intestine
2	chr20:13750600-13765000	Weak transcription	Gastric	stomach
3	chr20:13751200-13765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:13758800-13764800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr20:13761800-13764800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr20:13763200-13764800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr20:13763600-13764800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr20:13763600-13766600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr20:13763800-13767600	Active TSS	K562	blood
10	chr20:13764000-13764800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr20:13764000-13764800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr20:13764000-13764800	Enhancers	Brain Substantia Nigra	brain
13	chr20:13764000-13765000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr20:13764000-13766800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr20:13764000-13766800	Active TSS	HMEC	breast
16	chr20:13764000-13767000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr20:13764000-13767800	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr20:13764200-13764800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:13764200-13764800	Enhancers	Primary B cells from peripheral blood	blood
20	chr20:13764200-13764800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr20:13764200-13764800	Enhancers	Primary hematopoietic stem cells	blood
22	chr20:13764200-13764800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr20:13764200-13764800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr20:13764200-13764800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr20:13764200-13764800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr20:13764200-13764800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr20:13764200-13764800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr20:13764200-13764800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr20:13764200-13764800	Enhancers	Aorta	Aorta
30	chr20:13764200-13764800	Enhancers	Brain Hippocampus Middle	brain
31	chr20:13764200-13764800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr20:13764200-13764800	Enhancers	Colonic Mucosa	Colon
33	chr20:13764200-13764800	Enhancers	Colon Smooth Muscle	Colon
34	chr20:13764200-13764800	Enhancers	Esophagus	oesophagus
35	chr20:13764200-13764800	Enhancers	Fetal Heart	heart
36	chr20:13764200-13764800	Enhancers	Left Ventricle	heart
37	chr20:13764200-13764800	Enhancers	Lung	lung
38	chr20:13764200-13764800	Enhancers	Ovary	ovary
39	chr20:13764200-13764800	Enhancers	Pancreas	Pancrea
40	chr20:13764200-13764800	Enhancers	Placenta Amnion	Placenta Amnion
41	chr20:13764200-13764800	Enhancers	Right Atrium	heart
42	chr20:13764200-13764800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr20:13764200-13764800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr20:13764200-13764800	Enhancers	Thymus	Thymus
45	chr20:13764200-13764800	Enhancers	Spleen	Spleen
46	chr20:13764200-13764800	Flanking Active TSS	Dnd41	blood
47	chr20:13764200-13764800	Flanking Active TSS	Osteobl	bone
48	chr20:13764200-13765000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr20:13764200-13765000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr20:13764200-13765200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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