Variant report

Variant	rs1546653
Chromosome Location	chr4:48699542-48699543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48684102..48685627-chr4:48698753..48700458,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10433725	1.00[AMR][1000 genomes]
rs10938540	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12499963	0.83[AFR][1000 genomes]
rs12650202	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1949423	1.00[AMR][1000 genomes]
rs2056197	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2056200	1.00[AMR][1000 genomes]
rs2138868	1.00[AMR][1000 genomes]
rs2354313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2354315	1.00[AMR][1000 genomes]
rs6845398	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7436127	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7667909	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7690793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs938789	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv999203	chr4:48645887-48735512	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1802666	chr4:48646594-48721327	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013914	chr4:48652784-48728934	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv537090	chr4:48652784-48728934	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1796692	chr4:48686817-48726266	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1792683	chr4:48686817-48764009	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1795181	chr4:48686817-48764009	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48663600-48700200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:48670200-48700000	Weak transcription	Esophagus	oesophagus
4	chr4:48670200-48702000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:48670200-48702000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:48679000-48700000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:48680600-48699600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:48683400-48699600	Weak transcription	Psoas Muscle	Psoas
9	chr4:48683600-48700000	Weak transcription	Fetal Intestine Large	intestine
10	chr4:48683600-48700400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:48685000-48700400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:48686400-48699600	Weak transcription	Placenta	Placenta
13	chr4:48686400-48700000	Weak transcription	Dnd41	blood
14	chr4:48686800-48700200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:48686800-48708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:48687000-48700000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr4:48687000-48700000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:48687000-48701000	Weak transcription	GM12878-XiMat	blood
19	chr4:48687000-48708400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:48687200-48700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:48687200-48708400	Weak transcription	Primary B cells from cord blood	blood
22	chr4:48690200-48705200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:48690400-48700000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:48691400-48700400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:48691600-48699600	Weak transcription	HSMM	muscle
26	chr4:48691600-48710400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:48691800-48700000	Weak transcription	Liver	Liver
28	chr4:48692600-48700000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:48693600-48700200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:48694200-48699600	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:48694400-48700600	Weak transcription	Fetal Kidney	kidney
32	chr4:48694600-48699600	Weak transcription	HUVEC	blood vessel
33	chr4:48694800-48700000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:48694800-48700000	Weak transcription	Fetal Intestine Small	intestine
35	chr4:48695000-48699600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:48695200-48699600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:48695200-48699800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:48695200-48699800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:48695200-48699800	Weak transcription	NH-A	brain
40	chr4:48695200-48700400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr4:48695400-48711200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:48696000-48700000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:48696000-48700200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:48696000-48700600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:48696200-48699800	Weak transcription	Primary T cells from cord blood	blood
46	chr4:48696200-48699800	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:48696200-48700000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:48696200-48700000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:48696200-48700000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr4:48696200-48700200	Weak transcription	H1 Cell Line	embryonic stem cell

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