Variant report

Variant	rs55670663
Chromosome Location	chr4:48031169-48031170
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48029512..48031453-chr4:48088999..48090541,2	K562	blood:
2	chr4:48017249..48021049-chr4:48030612..48033189,3	MCF-7	breast:
3	chr4:48021540..48023440-chr4:48027193..48032829,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198515	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13116684	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13121957	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13140968	0.86[AFR][1000 genomes]
rs13145218	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150783	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13151608	0.93[ASN][1000 genomes]
rs224799	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321622	0.89[AFR][1000 genomes]
rs321632	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs321634	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321635	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35085584	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695325	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6447609	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6811245	0.81[AFR][1000 genomes]
rs6812991	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7674929	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55670663	CNGA1	cis	Thyroid	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48033800	Weak transcription	Pancreas	Pancrea
2	chr4:48019800-48033800	Weak transcription	Hela-S3	cervix
3	chr4:48019800-48034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:48019800-48034200	Weak transcription	HepG2	liver
5	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
7	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
8	chr4:48021600-48034200	Weak transcription	Stomach Mucosa	stomach
9	chr4:48024600-48043600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:48025400-48035000	Weak transcription	NHEK	skin
11	chr4:48026200-48031200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:48026800-48031200	Strong transcription	Liver	Liver
13	chr4:48026800-48045400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:48027200-48032800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:48027600-48031600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:48028000-48033800	Weak transcription	Fetal Lung	lung
17	chr4:48028200-48032000	Weak transcription	Fetal Intestine Large	intestine
18	chr4:48028200-48040800	Weak transcription	Gastric	stomach
19	chr4:48028200-48042600	Weak transcription	Placenta	Placenta
20	chr4:48028400-48031200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:48028400-48037400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:48029000-48032000	Weak transcription	Fetal Intestine Small	intestine
23	chr4:48029400-48033000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr4:48030000-48033800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:48030000-48034000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:48030200-48031600	Flanking Active TSS	GM12878-XiMat	blood
27	chr4:48030200-48033000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr4:48030200-48033000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr4:48030400-48032600	Weak transcription	Psoas Muscle	Psoas
30	chr4:48030400-48033000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr4:48030400-48034000	Enhancers	Fetal Heart	heart
32	chr4:48030400-48034200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:48030800-48031400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr4:48030800-48031400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr4:48030800-48032600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:48031000-48031400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr4:48031000-48031600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr4:48031000-48031800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:48031000-48032600	Weak transcription	HMEC	breast
40	chr4:48031000-48034200	Weak transcription	Rectal Mucosa Donor 31	rectum

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