Variant report

Variant	rs60514033
Chromosome Location	chr4:2966375-2966376
allele	A/G
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	chr4:2963047-2966632	MCF10A-Er-Src	breast:	n/a	n/a
2	REST	chr4:2964401-2966434	H1-neurons	neurons:	n/a	chr4:2966040-2966053 chr4:2965157-2965171 chr4:2965686-2965699 chr4:2964683-2964701
3	MXI1	chr4:2963508-2966390	IMR90	lung:	n/a	n/a
4	MXI1	chr4:2963015-2966472	SK-N-SH	brain:	n/a	n/a
5	RUNX3	chr4:2965866-2966542	GM12878	blood:	n/a	n/a
6	MTA3	chr4:2966004-2966562	GM12878	blood:	n/a	n/a
7	RUNX3	chr4:2966174-2966472	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2756517..2759780-chr4:2963075..2966456,5	K562	blood:
2	chr4:2962932..2965178-chr4:2965934..2967449,2	MCF-7	breast:
3	chr4:2936328..2940860-chr4:2961848..2966602,8	K562	blood:
4	chr4:2963799..2967429-chr4:2967585..2973552,6	K562	blood:
5	chr4:2845175..2847151-chr4:2963481..2966387,2	MCF-7	breast:
6	chr4:2965936..2968451-chr4:2977512..2979704,2	K562	blood:
7	chr4:2965958..2968897-chr4:2971775..2974450,2	MCF-7	breast:

Variant related genes	Relation type
NOP14	TF binding region
GRK4	TF binding region
ENSG00000125388	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs16843459	1.00[AMR][1000 genomes]
rs16843490	1.00[AMR][1000 genomes]
rs16843682	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35304823	1.00[AMR][1000 genomes]
rs35983864	1.00[AMR][1000 genomes]
rs55676948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55909241	1.00[AFR][1000 genomes]
rs56204916	1.00[AFR][1000 genomes]
rs56315133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57551202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57960709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58112051	1.00[AFR][1000 genomes]
rs58279895	1.00[AMR][1000 genomes]
rs58479563	1.00[AFR][1000 genomes]
rs58555511	1.00[AFR][1000 genomes]
rs58936143	1.00[AFR][1000 genomes]
rs60480235	1.00[AFR][1000 genomes]
rs60745500	1.00[AMR][1000 genomes]
rs61377156	1.00[AFR][1000 genomes]
rs61652297	1.00[AMR][1000 genomes]
rs61747144	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6830234	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6837197	1.00[AFR][1000 genomes]
rs6840149	1.00[AFR][1000 genomes]
rs6852880	1.00[AFR][1000 genomes]
rs73792109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792115	1.00[AMR][1000 genomes]
rs73792116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792119	0.89[AFR][1000 genomes]
rs73792122	1.00[AFR][1000 genomes]
rs73794816	1.00[AMR][1000 genomes]
rs73794824	1.00[AMR][1000 genomes]
rs73794825	1.00[AMR][1000 genomes]
rs73794827	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7657843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7676937	1.00[AMR][1000 genomes]
rs7699427	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv1008436	chr4:2947160-3031195	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv536998	chr4:2947160-3031195	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv593438	chr4:2948456-3030097	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1008527	chr4:2957814-3019042	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1014013	chr4:2959876-3009507	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv536999	chr4:2959876-3009507	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv878453	chr4:2963222-3021383	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1008781	chr4:2964080-3019042	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv1003528	chr4:2964261-3011568	Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv537000	chr4:2964261-3011568	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	esv3406626	chr4:2964379-2966927	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2963000-2966400	Active TSS	Psoas Muscle	Psoas
2	chr4:2963200-2966800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:2963400-2966400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr4:2963600-2966400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:2963800-2966400	Active TSS	Fetal Kidney	kidney
6	chr4:2964000-2966400	Active TSS	Ovary	ovary
7	chr4:2964000-2966400	Active TSS	A549	lung
8	chr4:2964000-2966800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:2964200-2966400	Active TSS	Left Ventricle	heart
10	chr4:2964200-2966400	Active TSS	Pancreas	Pancrea
11	chr4:2964200-2966400	Active TSS	HSMMtube	muscle
12	chr4:2964400-2966400	Active TSS	Colonic Mucosa	Colon
13	chr4:2964400-2966400	Active TSS	Fetal Lung	lung
14	chr4:2964400-2966400	Active TSS	HSMM	muscle
15	chr4:2964400-2966600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:2964400-2966800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:2965600-2966400	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr4:2965800-2966400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr4:2965800-2966400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr4:2965800-2966400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr4:2965800-2966400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr4:2965800-2966400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr4:2965800-2966400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr4:2965800-2966400	Active TSS	Brain Germinal Matrix	brain
25	chr4:2965800-2966400	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr4:2965800-2966400	Flanking Active TSS	Placenta	Placenta
27	chr4:2965800-2966400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr4:2965800-2966600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
29	chr4:2965800-2966600	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr4:2965800-2966600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:2965800-2966600	Active TSS	Right Atrium	heart
32	chr4:2965800-2966800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:2965800-2966800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:2965800-2967200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr4:2966000-2966400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr4:2966000-2966400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
37	chr4:2966000-2966400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:2966000-2966400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:2966000-2966400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:2966000-2966400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:2966000-2966400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:2966000-2966400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
43	chr4:2966000-2966400	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr4:2966000-2966400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:2966000-2966400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr4:2966000-2966400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr4:2966000-2966400	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr4:2966000-2966400	Flanking Active TSS	Liver	Liver
49	chr4:2966000-2966400	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr4:2966000-2966400	Flanking Active TSS	Brain Cingulate Gyrus	brain

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