Variant report

Variant	rs321630
Chromosome Location	chr4:48018170-48018171
allele	C/T
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	RAD21	chr4:48018163-48018609	H1-hESC	embryonic stem cell:	n/a	chr4:48018447-48018466
2	TCF12	chr4:48018136-48019597	ECC-1	luminal epithelium:	n/a	chr4:48018588-48018598
3	FOXA2	chr4:48018156-48018466	HepG2	liver:	n/a	n/a
4	STAT5A	chr4:48018104-48018656	GM12878	blood:	n/a	chr4:48018112-48018119 chr4:48018481-48018501 chr4:48018105-48018119
5	CTCF	chr4:48018126-48018765	K562	blood:	n/a	n/a
6	CTCF	chr4:48017913-48019455	SK-N-SH	brain:	n/a	n/a
7	FOXA1	chr4:48017703-48018538	HepG2	liver:	n/a	n/a
8	HDAC2	chr4:48018115-48018973	HepG2	liver:	n/a	n/a
9	CTCF	chr4:48018130-48018777	MCF-7	breast:	n/a	n/a
10	REST	chr4:48018146-48019722	H1-neurons	neurons:	n/a	chr4:48018731-48018744 chr4:48018257-48018266 chr4:48018524-48018531
11	ELF1	chr4:48018147-48019831	GM12878	blood:	n/a	n/a
12	FOXA1	chr4:48018147-48018536	HepG2	liver:	n/a	n/a
13	CTCF	chr4:48018138-48018807	A549	lung:	n/a	n/a
14	CTCF	chr4:48018056-48018913	HCT-116	colon:	n/a	n/a
15	TCF12	chr4:48018079-48019092	ECC-1	luminal epithelium:	n/a	chr4:48018588-48018598
16	CTCF	chr4:48018147-48018671	MCF-7	breast:	n/a	n/a
17	MXI1	chr4:48018104-48018957	HepG2	liver:	n/a	n/a
18	HNF4G	chr4:48018102-48018495	HepG2	liver:	n/a	chr4:48018287-48018302 chr4:48018287-48018302 chr4:48018285-48018300 chr4:48018287-48018302 chr4:48018287-48018301
19	NFIC	chr4:48018082-48019067	GM12878	blood:	n/a	n/a
20	RAD21	chr4:48018163-48018649	H1-hESC	embryonic stem cell:	n/a	chr4:48018447-48018466
21	POLR2A	chr4:48018149-48019426	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr4:48018154-48018878	HepG2	liver:	n/a	chr4:48018731-48018744 chr4:48018257-48018266 chr4:48018524-48018531
23	HNF4A	chr4:48018132-48018424	HepG2	liver:	n/a	chr4:48018287-48018302 chr4:48018287-48018302 chr4:48018286-48018301 chr4:48018287-48018302 chr4:48018287-48018301
24	ARID3A	chr4:48018132-48018188	HepG2	liver:	n/a	n/a
25	MYBL2	chr4:48018138-48018764	HepG2	liver:	n/a	n/a
26	PML	chr4:48018104-48019724	GM12878	blood:	n/a	n/a
27	FOXA1	chr4:48018099-48018927	HepG2	liver:	n/a	n/a
28	JUN	chr4:48018089-48019548	K562	blood:	n/a	chr4:48018779-48018788 chr4:48019256-48019267 chr4:48019253-48019264
29	HNF4A	chr4:48018131-48018458	HepG2	liver:	n/a	chr4:48018287-48018302 chr4:48018287-48018302 chr4:48018286-48018301 chr4:48018287-48018302 chr4:48018287-48018301
30	ZEB1	chr4:48017689-48019513	HepG2	liver:	n/a	n/a
31	KAP1	chr4:48018033-48019485	HEK293	kidney:	n/a	n/a
32	SIN3A	chr4:48018046-48019563	H1-hESC	embryonic stem cell:	n/a	chr4:48018690-48018699

No.	Distal block	Cell Line	Cell type
1	chr4:48016518..48018197-chr4:48024501..48026849,2	K562	blood:
2	chr4:47915045..47916605-chr4:48017433..48018940,2	MCF-7	breast:
3	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:
4	chr4:48015687..48018286-chr4:48032689..48034980,2	K562	blood:

Variant related genes	Relation type
CNGA1	TF binding region
NIPAL1	TF binding region
ENSG00000170448	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11722463	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11733284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11736427	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13116684	0.82[ASW][hapmap]
rs13120847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13125949	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13140968	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13142905	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13146880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1507922	0.88[JPT][hapmap]
rs224799	0.85[AFR][1000 genomes]
rs321620	0.88[JPT][hapmap]
rs321622	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]
rs321628	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321632	0.88[ASW][hapmap];0.85[LWK][hapmap];0.81[AFR][1000 genomes]
rs321634	0.94[AFR][1000 genomes]
rs321635	0.81[AFR][1000 genomes]
rs4694879	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4695325	0.81[AFR][1000 genomes]
rs4695328	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6811245	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6832503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6835057	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs98270	0.99[AFR][1000 genomes];0.91[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs321630	CNGA1	cis	Esophagus Muscularis	GTEx
rs321630	CNGA1	cis	Adipose Subcutaneous	GTEx
rs321630	CNGA1	cis	Muscle Skeletal	GTEx
rs321630	CNGA1	cis	Artery Tibial	GTEx
rs321630	CNGA1	cis	Thyroid	GTEx
rs321630	CNGA1	cis	Heart Left Ventricle	GTEx
rs321630	JPH1	trans	cerebellum	SCAN
rs321630	CNGA1	cis	Artery Aorta	GTEx
rs321630	NIPAL1	cis	lung	GTEx
rs321630	NFXL1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48011800-48018200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48017200-48018200	Active TSS	Fetal Intestine Large	intestine
3	chr4:48017400-48018200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr4:48017400-48019200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:48017400-48020200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:48017600-48018200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:48017600-48018200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr4:48017600-48018200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:48017600-48018200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr4:48017600-48018200	Active TSS	Placenta	Placenta
11	chr4:48017600-48018200	Active TSS	Fetal Stomach	stomach
12	chr4:48017600-48018200	Enhancers	Pancreas	Pancrea
13	chr4:48017600-48018200	Enhancers	Psoas Muscle	Psoas
14	chr4:48017600-48018400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr4:48017600-48018400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr4:48017600-48018400	Flanking Active TSS	Stomach Mucosa	stomach
17	chr4:48017600-48019000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr4:48017600-48019000	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr4:48017600-48019200	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr4:48017600-48020600	Active TSS	Rectal Smooth Muscle	rectum
21	chr4:48017800-48018200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr4:48017800-48018200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:48017800-48018200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr4:48017800-48018200	Active TSS	Colonic Mucosa	Colon
25	chr4:48017800-48018200	Enhancers	Gastric	stomach
26	chr4:48017800-48018200	Enhancers	Spleen	Spleen
27	chr4:48017800-48018200	Flanking Active TSS	GM12878-XiMat	blood
28	chr4:48017800-48018400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr4:48017800-48018600	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr4:48017800-48018800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:48017800-48019000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr4:48017800-48019200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:48017800-48019600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr4:48017800-48019800	Active TSS	Esophagus	oesophagus
35	chr4:48017800-48019800	Active TSS	Fetal Kidney	kidney
36	chr4:48018000-48018200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
37	chr4:48018000-48018200	Bivalent Enhancer	Primary B cells from cord blood	blood
38	chr4:48018000-48018200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr4:48018000-48018200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:48018000-48018200	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:48018000-48018200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:48018000-48018200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:48018000-48018200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:48018000-48018200	Active TSS	Liver	Liver
45	chr4:48018000-48018200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
46	chr4:48018000-48018200	Enhancers	Brain Hippocampus Middle	brain
47	chr4:48018000-48018200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr4:48018000-48018200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr4:48018000-48018200	Bivalent Enhancer	Fetal Thymus	thymus
50	chr4:48018000-48018200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle

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