Variant report

Variant	rs4787643
Chromosome Location	chr16:30393660-30393661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30389715..30395001-chr16:30417296..30421020,7	K562	blood:
2	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
3	chr16:30387676..30396507-chr16:30404234..30411930,28	K562	blood:
4	chr16:30393486..30397071-chr16:30402673..30407150,6	MCF-7	breast:
5	chr16:30078555..30080621-chr16:30391521..30394276,2	MCF-7	breast:
6	chr16:30364024..30368341-chr16:30387690..30394486,12	K562	blood:
7	chr16:30384243..30394929-chr16:30405602..30409736,14	K562	blood:
8	chr16:30365775..30369229-chr16:30392373..30394486,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000149925	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000260219	Chromatin interaction
ENSG00000179965	Chromatin interaction
ENSG00000169217	Chromatin interaction
ENSG00000180035	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11150586	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs11642676	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11645581	0.90[EUR][1000 genomes]
rs11646130	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11862806	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11863150	0.96[CEU][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs12446288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12447833	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12921440	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs12930787	0.87[EUR][1000 genomes]
rs13333093	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs35480350	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35598865	1.00[JPT][hapmap]
rs3574	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4465620	0.88[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs4787642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4788409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788410	0.82[EUR][1000 genomes]
rs4788411	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4788413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788414	0.85[EUR][1000 genomes]
rs62055459	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6565180	0.88[EUR][1000 genomes]
rs6565182	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6565183	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs68051857	0.86[EUR][1000 genomes]
rs7203359	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73532600	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8046445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8049108	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs8050812	1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8051096	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs8060853	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9888967	0.92[ASN][1000 genomes]
rs9921711	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv962197	chr16:30390489-30425618	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv1782	chr16:30391812-30410266	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4787643	LOC440354	cis	lymphoblastoid	seeQTL
rs4787643	TBX6	cis	parietal	SCAN
rs4787643	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs4787643	LOC595101	cis	lymphoblastoid	seeQTL
rs4787643	GDPD3	cis	cerebellum	SCAN
rs4787643	SEPHS2	cis	cerebellum	SCAN
rs4787643	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL
rs4787643	MAPK3	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30390600-30394000	Weak transcription	Aorta	Aorta
2	chr16:30390800-30395200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr16:30390800-30405600	Weak transcription	Right Atrium	heart
4	chr16:30391000-30393800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:30391000-30393800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:30391000-30394000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr16:30391000-30394200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr16:30391000-30395000	Weak transcription	Fetal Lung	lung
9	chr16:30391000-30405000	Weak transcription	NHLF	lung
10	chr16:30391000-30405200	Weak transcription	Fetal Brain Female	brain
11	chr16:30391000-30405400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr16:30391400-30394000	Weak transcription	Colon Smooth Muscle	Colon
13	chr16:30391400-30394200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr16:30391400-30396800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr16:30392000-30393800	Weak transcription	Brain Hippocampus Middle	brain
16	chr16:30392000-30394400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr16:30392000-30395800	Enhancers	Fetal Muscle Trunk	muscle
18	chr16:30392200-30393800	Enhancers	Placenta	Placenta
19	chr16:30392200-30394600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr16:30392200-30394600	Flanking Active TSS	GM12878-XiMat	blood
21	chr16:30392200-30395000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr16:30392200-30395600	Enhancers	Fetal Muscle Leg	muscle
23	chr16:30392400-30394000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr16:30392400-30394000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:30392400-30394200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr16:30392400-30394400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr16:30392400-30394600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr16:30392400-30394800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr16:30392400-30397800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr16:30392600-30393800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr16:30392600-30394200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr16:30392600-30394400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr16:30392600-30395200	Flanking Active TSS	Dnd41	blood
34	chr16:30392800-30394200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr16:30392800-30394200	Active TSS	Rectal Smooth Muscle	rectum
36	chr16:30392800-30394400	Enhancers	Primary hematopoietic stem cells	blood
37	chr16:30393000-30393800	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr16:30393000-30393800	Enhancers	Brain Germinal Matrix	brain
39	chr16:30393000-30393800	Active TSS	Stomach Smooth Muscle	stomach
40	chr16:30393000-30394400	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr16:30393000-30394600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr16:30393000-30394600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr16:30393000-30394800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr16:30393200-30393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr16:30393200-30393800	Enhancers	HepG2	liver
46	chr16:30393200-30394000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr16:30393200-30394400	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr16:30393200-30394400	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr16:30393200-30394600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr16:30393200-30394800	Weak transcription	Fetal Stomach	stomach

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