Variant report

Variant	rs4487645
Chromosome Location	chr7:21938240-21938241
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21938160..21940188-chr7:21943715..21946302,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164649	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1128226	0.83[ASN][1000 genomes]
rs11761264	0.82[GIH][hapmap]
rs11763022	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11763025	0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11763665	0.88[AMR][1000 genomes]
rs11763709	0.88[AMR][1000 genomes]
rs11769521	0.83[MEX][hapmap];0.88[AMR][1000 genomes]
rs12540021	0.96[GIH][hapmap];0.81[LWK][hapmap];0.85[ASN][1000 genomes]
rs17361667	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4636103	0.87[MEX][hapmap]
rs55714084	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56249828	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56333627	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57104699	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6948632	0.86[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7785157	0.92[EUR][1000 genomes]
rs7971	0.86[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Multiple myeloma	22120009	GWAS catalog
Multiple myeloma (hyperdiploidy)	23502783	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4487645	TWIST1	cis	cerebellum	SCAN
rs4487645	SP8	cis	cerebellum	SCAN
rs4487645	ADAMTSL5	trans	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21910000-21939400	Weak transcription	Left Ventricle	heart
2	chr7:21911200-21938400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:21917000-21938400	Weak transcription	Fetal Intestine Small	intestine
4	chr7:21923200-21938600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:21924400-21945400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:21926600-21942600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:21926800-21939200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:21927800-21938400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:21927800-21940200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:21928000-21942600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:21928200-21938600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:21928200-21939600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:21928800-21938400	Weak transcription	NHDF-Ad	bronchial
14	chr7:21930800-21938400	Weak transcription	Esophagus	oesophagus
15	chr7:21931000-21942400	Weak transcription	Fetal Kidney	kidney
16	chr7:21932600-21938400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:21932600-21938400	Weak transcription	Brain Anterior Caudate	brain
18	chr7:21932600-21942000	Weak transcription	Brain Germinal Matrix	brain
19	chr7:21932600-21951000	Weak transcription	HSMM	muscle
20	chr7:21932800-21938800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:21933000-21963200	Weak transcription	A549	lung
22	chr7:21933600-21939000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:21934000-21950400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:21934200-21951600	Weak transcription	Fetal Brain Male	brain
25	chr7:21935200-21942200	Weak transcription	HMEC	breast
26	chr7:21936400-21942400	Weak transcription	NH-A	brain
27	chr7:21936600-21938400	Weak transcription	NHLF	lung
28	chr7:21936600-21938600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:21936600-21939000	Weak transcription	Fetal Intestine Large	intestine
30	chr7:21936600-21942000	Weak transcription	HSMMtube	muscle
31	chr7:21936600-21956400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr7:21936600-21956600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr7:21936800-21938400	Weak transcription	Ovary	ovary
34	chr7:21936800-21938400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr7:21936800-21939000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:21936800-21945200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:21936800-21945200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr7:21937000-21939000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:21937000-21939000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr7:21937000-21942200	Weak transcription	Brain Angular Gyrus	brain
41	chr7:21937000-21952200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:21937000-21956400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:21937200-21938800	Genic enhancers	Fetal Thymus	thymus
44	chr7:21937200-21939800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:21937200-21956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr7:21937400-21940800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:21937400-21950800	Weak transcription	Right Atrium	heart
48	chr7:21937400-21956000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:21937600-21938400	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr7:21937600-21938400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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