Variant report

Variant	rs7683704
Chromosome Location	chr4:100004226-100004227
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	POLR2A	chr4:100003973-100004412	K562	blood:	n/a	n/a
2	HEY1	chr4:100004117-100004332	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:100004075-100004457	HepG2	liver:	n/a	n/a
4	MAFK	chr4:100004203-100004399	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:100004188-100004356	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:100004027-100005209	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:100004145-100004391	HepG2	liver:	n/a	n/a
8	POLR2A	chr4:100004049-100006136	K562	blood:	n/a	n/a

Variant related genes	Relation type
ADH5	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1061187	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1154400	0.88[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs1154401	0.91[YRI][hapmap]
rs11547772	1.00[CEU][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12106	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1230155	0.93[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12697	0.91[ASW][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1311620	0.91[YRI][hapmap]
rs13118409	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13119035	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13120000	0.88[CEU][hapmap]
rs13125919	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13145727	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13146416	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17595424	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1803037	1.00[CEU][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28730587	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730591	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730592	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730595	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730602	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28730605	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730632	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34766933	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699699	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699700	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4699701	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6852848	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658118	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658127	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658279	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7662987	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7669660	0.91[ASW][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7683802	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7684735	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7684986	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7683704	ADH5	cis	Whole Blood	GTEx
rs7683704	ADH7	cis	parietal	SCAN
rs7683704	ADH5	cis	parietal	SCAN
rs7683704	ADH5	cis	cerebellum	SCAN

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	chr4:99985600-100005200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:99985600-100006600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:99987200-100005000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:99987200-100005400	Strong transcription	Dnd41	blood
10	chr4:99987200-100006600	Strong transcription	HSMM	muscle
11	chr4:99987200-100008000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:99987400-100007600	Strong transcription	Fetal Thymus	thymus
13	chr4:99987600-100006000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:99987600-100006600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:99987800-100006800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:99987800-100007000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:99988000-100006800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:99988000-100007000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:99988200-100006400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:99988400-100007000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:99989000-100006600	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr4:99989000-100006800	Strong transcription	Primary T cells from cord blood	blood
23	chr4:99989400-100007400	Strong transcription	HMEC	breast
24	chr4:99989600-100007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:99990000-100005000	Strong transcription	Placenta	Placenta
26	chr4:99990400-100005600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:99990400-100006400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr4:99990600-100007200	Strong transcription	Osteobl	bone
29	chr4:99990600-100007400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:99990800-100007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:99991000-100006200	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:99991200-100006000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:99991200-100006800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr4:99991200-100007000	Strong transcription	Primary B cells from cord blood	blood
35	chr4:99991200-100007400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:99991200-100007400	Strong transcription	NHDF-Ad	bronchial
37	chr4:99991400-100006600	Strong transcription	Fetal Intestine Large	intestine
38	chr4:99991400-100006800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr4:99991400-100006800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:99991400-100007000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr4:99991400-100007000	Strong transcription	Thymus	Thymus
42	chr4:99991400-100007000	Strong transcription	HUVEC	blood vessel
43	chr4:99991400-100007400	Strong transcription	Fetal Lung	lung
44	chr4:99991600-100006600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:99991600-100006800	Strong transcription	K562	blood
46	chr4:99991600-100007000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:99992400-100006400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr4:99992400-100007200	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr4:99992400-100007200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:99992400-100007200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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