Variant report

Variant	rs321622
Chromosome Location	chr4:48024380-48024381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:47931421..47933962-chr4:48023489..48026018,2	MCF-7	breast:
2	chr4:48019190..48021605-chr4:48023120..48025588,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11722463	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11733284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11736427	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13116684	0.87[ASW][hapmap]
rs13120847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125949	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140968	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13142905	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13145218	0.88[AFR][1000 genomes]
rs13146880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13150783	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs1507922	0.88[JPT][hapmap]
rs224799	0.97[AFR][1000 genomes]
rs321620	0.88[JPT][hapmap]
rs321628	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321630	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321631	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321632	0.81[ASW][hapmap]
rs321634	0.83[AFR][1000 genomes]
rs4694879	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695325	0.93[AFR][1000 genomes]
rs4695328	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55670663	0.89[AFR][1000 genomes]
rs6811245	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812991	0.80[AFR][1000 genomes]
rs6832503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835057	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7674929	0.80[AFR][1000 genomes]
rs98270	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs321622	CNGA1	cis	Adipose Subcutaneous	GTEx
rs321622	CNGA1	cis	Esophagus Muscularis	GTEx
rs321622	JPH1	trans	cerebellum	SCAN
rs321622	CNGA1	cis	Muscle Skeletal	GTEx
rs321622	CNGA1	cis	Thyroid	GTEx
rs321622	BAI2	trans	parietal	SCAN
rs321622	CNGA1	cis	Heart Left Ventricle	GTEx
rs321622	NIPAL1	cis	lung	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48024400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:48019800-48026000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:48019800-48026600	Weak transcription	NH-A	brain
4	chr4:48019800-48027600	Weak transcription	Placenta	Placenta
5	chr4:48019800-48030200	Weak transcription	Psoas Muscle	Psoas
6	chr4:48019800-48033800	Weak transcription	Pancreas	Pancrea
7	chr4:48019800-48033800	Weak transcription	Hela-S3	cervix
8	chr4:48019800-48034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:48019800-48034200	Weak transcription	HepG2	liver
10	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
12	chr4:48020000-48026600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:48020000-48029200	Weak transcription	GM12878-XiMat	blood
14	chr4:48020400-48027600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:48020600-48026200	Weak transcription	Fetal Heart	heart
16	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
17	chr4:48020800-48025000	Enhancers	Fetal Intestine Small	intestine
18	chr4:48020800-48025400	Enhancers	Fetal Intestine Large	intestine
19	chr4:48020800-48026600	Weak transcription	HMEC	breast
20	chr4:48021000-48026400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:48021600-48034200	Weak transcription	Stomach Mucosa	stomach
22	chr4:48021800-48026800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:48022200-48029800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:48022600-48024800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:48022600-48025200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr4:48022600-48026600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:48022800-48025600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr4:48022800-48026600	Weak transcription	Gastric	stomach
29	chr4:48022800-48026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:48022800-48029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:48023200-48027000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:48023400-48025000	Enhancers	Duodenum Mucosa	Duodenum
33	chr4:48023400-48026800	Weak transcription	Liver	Liver
34	chr4:48024200-48024600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:48024200-48024600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:48024200-48024600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr4:48024200-48025400	Strong transcription	NHEK	skin

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