Variant report

Variant	rs321621
Chromosome Location	chr4:48023573-48023574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:48023251-48023620	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:48018009..48020666-chr4:48022242..48023763,2	K562	blood:
2	chr4:47931421..47933962-chr4:48023489..48026018,2	MCF-7	breast:
3	chr4:48019190..48021605-chr4:48023120..48025588,2	K562	blood:

Variant related genes	Relation type
NIPAL1	TF binding region
CNGA1	TF binding region
ENSG00000198515	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 34 )
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];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10805163	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10938520	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11733288	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645245	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1396051	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507913	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1507914	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs178650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1837518	0.89[ASN][1000 genomes]
rs188901	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[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];0.86[ASN][1000 genomes]
rs2661513	0.80[AFR][1000 genomes]
rs28578328	0.80[ASN][1000 genomes]
rs28699496	0.82[ASN][1000 genomes]
rs3113881	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113882	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs321623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321633	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694880	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685636	0.92[AFR][1000 genomes];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs321621	NFXL1	cis	Whole Blood	GTEx
rs321621	CNGA1	cis	Muscle Skeletal	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48024200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:48019800-48024400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:48019800-48026000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:48019800-48026600	Weak transcription	NH-A	brain
5	chr4:48019800-48027600	Weak transcription	Placenta	Placenta
6	chr4:48019800-48030200	Weak transcription	Psoas Muscle	Psoas
7	chr4:48019800-48033800	Weak transcription	Pancreas	Pancrea
8	chr4:48019800-48033800	Weak transcription	Hela-S3	cervix
9	chr4:48019800-48034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:48019800-48034200	Weak transcription	HepG2	liver
11	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
13	chr4:48020000-48026600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:48020000-48029200	Weak transcription	GM12878-XiMat	blood
15	chr4:48020400-48027600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:48020600-48026200	Weak transcription	Fetal Heart	heart
17	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
18	chr4:48020800-48024200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:48020800-48025000	Enhancers	Fetal Intestine Small	intestine
20	chr4:48020800-48025400	Enhancers	Fetal Intestine Large	intestine
21	chr4:48020800-48026600	Weak transcription	HMEC	breast
22	chr4:48021000-48026400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:48021600-48034200	Weak transcription	Stomach Mucosa	stomach
24	chr4:48021800-48026800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:48022200-48029800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:48022400-48023600	Strong transcription	NHEK	skin
27	chr4:48022600-48024800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:48022600-48025200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr4:48022600-48026600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:48022800-48025600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr4:48022800-48026600	Weak transcription	Gastric	stomach
32	chr4:48022800-48026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:48022800-48029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:48023200-48027000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:48023400-48025000	Enhancers	Duodenum Mucosa	Duodenum
36	chr4:48023400-48026800	Weak transcription	Liver	Liver

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