Variant report

Variant	rs321628
Chromosome Location	chr4:48016875-48016876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48016518..48018197-chr4:48024501..48026849,2	K562	blood:
2	chr4:48015687..48018286-chr4:48032689..48034980,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11722463	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11733284	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11736427	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13120847	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13125949	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13140968	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13142905	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13146880	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs224799	0.85[AFR][1000 genomes]
rs321622	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321630	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321631	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321632	0.81[AFR][1000 genomes]
rs321634	0.94[AFR][1000 genomes]
rs321635	0.81[AFR][1000 genomes]
rs4694879	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4695325	0.81[AFR][1000 genomes]
rs4695328	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6811245	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6832503	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6835057	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs98270	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs321628	CNGA1	cis	Esophagus Muscularis	GTEx
rs321628	NIPAL1	cis	lung	GTEx
rs321628	CNGA1	cis	Heart Left Ventricle	GTEx
rs321628	CNGA1	cis	Artery Aorta	GTEx
rs321628	CNGA1	cis	Muscle Skeletal	GTEx
rs321628	CNGA1	cis	Artery Tibial	GTEx
rs321628	CNGA1	cis	Thyroid	GTEx
rs321628	CNGA1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48005400-48017400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:48008000-48017600	Weak transcription	Psoas Muscle	Psoas
3	chr4:48010200-48017200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:48010200-48017600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:48011000-48017400	Weak transcription	Colonic Mucosa	Colon
6	chr4:48011000-48017600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:48011000-48017600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:48011200-48017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:48011400-48017600	Weak transcription	Esophagus	oesophagus
10	chr4:48011800-48017800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:48011800-48018200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:48012800-48017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:48013200-48017200	Weak transcription	Liver	Liver
14	chr4:48013800-48017800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:48014200-48017800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:48014400-48017800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:48015200-48018000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:48015400-48017600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:48015600-48017600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:48015800-48017600	Enhancers	HepG2	liver
21	chr4:48016200-48017800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr4:48016400-48017000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:48016600-48017400	Enhancers	Fetal Intestine Small	intestine
24	chr4:48016600-48017800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:48016800-48017000	Enhancers	Fetal Intestine Large	intestine
26	chr4:48016800-48017400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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