Variant report

Variant	rs28730602
Chromosome Location	chr4:100001682-100001683
allele	A/C
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	chr4:99999919-100001969	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99915853..99918198-chr4:100001178..100002788,2	MCF-7	breast:

Variant related genes	Relation type
ADH5	TF binding region
ENSG00000164024	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1154400	0.82[AFR][1000 genomes]
rs11547772	0.82[AMR][1000 genomes]
rs12106	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1230155	0.87[AFR][1000 genomes]
rs12502237	0.81[AFR][1000 genomes]
rs12697	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28730632	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699700	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658118	0.82[AMR][1000 genomes]
rs7658279	0.82[AMR][1000 genomes]
rs7669660	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7683704	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7684735	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28730602	ADH5	Cis_1M	lymphoblastoid	RTeQTL

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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