Variant report

Variant	rs178650
Chromosome Location	chr4:48019859-48019860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48019190..48021605-chr4:48023120..48025588,2	K562	blood:
2	chr4:48019513..48022096-chr4:48074921..48077158,2	MCF-7	breast:
3	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163293	Chromatin interaction
ENSG00000170448	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10517204	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10805163	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10938520	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11733288	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12645245	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1396051	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1507913	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1507914	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1837518	0.89[ASN][1000 genomes]
rs188901	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1899060	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs224800	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2581493	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2661513	0.80[AFR][1000 genomes]
rs28578328	0.81[EUR][1000 genomes]
rs28699496	0.83[ASN][1000 genomes]
rs3113881	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3113882	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs321621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321642	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs321644	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs321646	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3950558	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694880	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6850603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7685636	0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013163	chr4:47977844-48022511	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537084	chr4:47977844-48022511	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs178650	CNGA1	cis	Muscle Skeletal	GTEx
rs178650	NFXL1	cis	Whole Blood	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48017400-48020200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr4:48017600-48020600	Active TSS	Rectal Smooth Muscle	rectum
3	chr4:48018000-48020000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:48018000-48020400	Active TSS	Duodenum Mucosa	Duodenum
5	chr4:48018000-48020600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:48018200-48020000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr4:48018400-48020400	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr4:48018600-48020000	Bivalent/Poised TSS	Fetal Stomach	stomach
9	chr4:48018600-48020200	Active TSS	HMEC	breast
10	chr4:48018600-48020600	Active TSS	Colonic Mucosa	Colon
11	chr4:48019000-48020000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr4:48019000-48020000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr4:48019000-48020000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:48019200-48020200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:48019400-48020600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr4:48019600-48020000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr4:48019600-48020000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:48019600-48020600	Flanking Active TSS	NHEK	skin
19	chr4:48019800-48020000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
20	chr4:48019800-48020000	Active TSS	GM12878-XiMat	blood
21	chr4:48019800-48020200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:48019800-48020200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:48019800-48020400	Weak transcription	Fetal Heart	heart
24	chr4:48019800-48020400	Active TSS	Fetal Intestine Large	intestine
25	chr4:48019800-48020400	Active TSS	Fetal Intestine Small	intestine
26	chr4:48019800-48020400	Enhancers	Stomach Mucosa	stomach
27	chr4:48019800-48020600	Enhancers	Liver	Liver
28	chr4:48019800-48022600	Weak transcription	Gastric	stomach
29	chr4:48019800-48022600	Weak transcription	Small Intestine	intestine
30	chr4:48019800-48024200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:48019800-48024400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:48019800-48026000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr4:48019800-48026600	Weak transcription	NH-A	brain
34	chr4:48019800-48027600	Weak transcription	Placenta	Placenta
35	chr4:48019800-48030200	Weak transcription	Psoas Muscle	Psoas
36	chr4:48019800-48033800	Weak transcription	Pancreas	Pancrea
37	chr4:48019800-48033800	Weak transcription	Hela-S3	cervix
38	chr4:48019800-48034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:48019800-48034200	Weak transcription	HepG2	liver
40	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus

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