Variant report

Variant	rs17001553
Chromosome Location	chr4:77090165-77090166
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	MYC	chr4:77090044-77090172	H1-hESC	embryonic stem cell:	n/a	chr4:77090087-77090096

Variant related genes	Relation type
SCARB2	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11934628	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11938219	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11941285	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11944780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001644	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001645	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001647	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001648	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001649	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2228380	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28655570	1.00[EUR][1000 genomes]
rs34078946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34647444	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34865218	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35211143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35634209	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35866970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4129291	1.00[AMR][1000 genomes]
rs56891967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58990415	1.00[EUR][1000 genomes]
rs59199771	1.00[EUR][1000 genomes]
rs59815580	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59876319	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60319873	1.00[EUR][1000 genomes]
rs60541751	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60744184	1.00[EUR][1000 genomes]
rs61079077	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61313750	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6832579	1.00[EUR][1000 genomes]
rs7672121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs999358	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs999359	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv470047	chr4:77033590-77096777	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1008318	chr4:77042356-77095658	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv537144	chr4:77042356-77095658	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1000539	chr4:77042356-77105492	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1000178	chr4:77053046-77113080	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77070400-77093400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:77070600-77113600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:77070800-77093800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:77071200-77113600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:77078200-77100600	Weak transcription	K562	blood
6	chr4:77078600-77100800	Strong transcription	Placenta	Placenta
7	chr4:77079200-77098000	Strong transcription	Fetal Muscle Leg	muscle
8	chr4:77079200-77100800	Strong transcription	Liver	Liver
9	chr4:77079400-77097200	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr4:77079400-77098800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:77079400-77100000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:77079400-77100800	Strong transcription	Fetal Intestine Large	intestine
13	chr4:77079400-77101400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr4:77079400-77108200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:77079600-77091000	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:77079600-77098800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:77079600-77099000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr4:77079600-77101200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr4:77079600-77101400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:77079800-77098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:77079800-77101000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:77080000-77091600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr4:77080400-77091400	Strong transcription	Osteobl	bone
24	chr4:77080400-77098400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:77080600-77113600	Weak transcription	Thymus	Thymus
26	chr4:77080800-77099000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:77080800-77101200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:77080800-77101200	Strong transcription	NHDF-Ad	bronchial
29	chr4:77081000-77097000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:77081000-77097400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:77081000-77097400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:77081400-77091200	Strong transcription	Adipose Nuclei	Adipose
33	chr4:77081400-77091400	Strong transcription	Fetal Brain Female	brain
34	chr4:77081400-77099200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr4:77081600-77091200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:77081600-77091400	Strong transcription	Left Ventricle	heart
37	chr4:77081600-77092000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:77081600-77097200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:77081600-77097400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:77082200-77091200	Strong transcription	Primary T cells from cord blood	blood
41	chr4:77082200-77091600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:77082200-77096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:77082200-77097400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:77082200-77098000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:77082400-77091400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr4:77082400-77098000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:77082400-77101400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:77082600-77090200	Strong transcription	Fetal Intestine Small	intestine
49	chr4:77082600-77090200	Strong transcription	Fetal Stomach	stomach
50	chr4:77082600-77091000	Strong transcription	HSMMtube	muscle

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