Variant report

Variant	rs28730610
Chromosome Location	chr4:100001102-100001103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs17028473	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028505	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364319	1.00[AMR][1000 genomes]
rs28730571	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28730641	0.90[AFR][1000 genomes]
rs28730643	0.90[AFR][1000 genomes]
rs28730644	0.90[AFR][1000 genomes]
rs28730645	0.90[AFR][1000 genomes]
rs28730649	0.87[AFR][1000 genomes]
rs29001339	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs29001631	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55820222	1.00[AMR][1000 genomes]
rs59728850	1.00[AMR][1000 genomes]
rs62325240	0.88[AFR][1000 genomes]
rs62325241	0.84[AFR][1000 genomes]
rs62325242	0.90[AFR][1000 genomes]
rs6532799	1.00[AMR][1000 genomes]
rs6827292	0.90[AFR][1000 genomes]
rs6828819	1.00[AMR][1000 genomes]
rs6831854	1.00[AMR][1000 genomes]
rs6835771	1.00[AMR][1000 genomes]
rs72897134	1.00[AMR][1000 genomes]
rs72901271	1.00[AMR][1000 genomes]
rs72901287	1.00[AMR][1000 genomes]
rs72901294	1.00[AMR][1000 genomes]
rs72901295	1.00[AMR][1000 genomes]
rs72909452	1.00[AMR][1000 genomes]
rs72909467	1.00[AMR][1000 genomes]
rs7664906	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7669447	1.00[AMR][1000 genomes]
rs7672509	1.00[AMR][1000 genomes]
rs7679102	0.90[AFR][1000 genomes]
rs7684674	1.00[AMR][1000 genomes]
rs7689911	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99977600-100008400	Weak transcription	Stomach Mucosa	stomach
2	chr4:99977800-100009000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:99978000-100007800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:99983000-100004600	Weak transcription	Pancreas	Pancrea
5	chr4:99983200-100008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:99983600-100003400	Weak transcription	Right Ventricle	heart
7	chr4:99985600-100005200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:99985600-100006600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:99987200-100005000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:99987200-100005400	Strong transcription	Dnd41	blood
11	chr4:99987200-100006600	Strong transcription	HSMM	muscle
12	chr4:99987200-100008000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:99987400-100007600	Strong transcription	Fetal Thymus	thymus
14	chr4:99987600-100006000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:99987600-100006600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:99987800-100006800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:99987800-100007000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:99988000-100006800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:99988000-100007000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:99988200-100006400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:99988400-100007000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:99988800-100001800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:99989000-100006600	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr4:99989000-100006800	Strong transcription	Primary T cells from cord blood	blood
25	chr4:99989400-100007400	Strong transcription	HMEC	breast
26	chr4:99989600-100007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:99990000-100005000	Strong transcription	Placenta	Placenta
28	chr4:99990400-100005600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:99990400-100006400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr4:99990600-100007200	Strong transcription	Osteobl	bone
31	chr4:99990600-100007400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:99990800-100007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:99991000-100006200	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:99991200-100006000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:99991200-100006800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:99991200-100007000	Strong transcription	Primary B cells from cord blood	blood
37	chr4:99991200-100007400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:99991200-100007400	Strong transcription	NHDF-Ad	bronchial
39	chr4:99991400-100006600	Strong transcription	Fetal Intestine Large	intestine
40	chr4:99991400-100006800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:99991400-100006800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:99991400-100007000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:99991400-100007000	Strong transcription	Thymus	Thymus
44	chr4:99991400-100007000	Strong transcription	HUVEC	blood vessel
45	chr4:99991400-100007400	Strong transcription	Fetal Lung	lung
46	chr4:99991600-100006600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:99991600-100006800	Strong transcription	K562	blood
48	chr4:99991600-100007000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:99992400-100006400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:99992400-100007200	Strong transcription	H1 Cell Line	embryonic stem cell

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