Variant report

Variant	rs321631
Chromosome Location	chr4:48018229-48018230
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	MAFF	chr4:48018192-48018385	HepG2	liver:	n/a	n/a
2	RAD21	chr4:48018175-48018657	HepG2	liver:	n/a	chr4:48018447-48018466
3	RAD21	chr4:48018163-48018609	H1-hESC	embryonic stem cell:	n/a	chr4:48018447-48018466
4	RAD21	chr4:48018175-48018657	ECC-1	luminal epithelium:	n/a	chr4:48018447-48018466
5	TCF12	chr4:48018136-48019597	ECC-1	luminal epithelium:	n/a	chr4:48018588-48018598
6	SETDB1	chr4:48018229-48018666	U2OS	brain:	n/a	n/a
7	BCLAF1	chr4:48018183-48019163	GM12878	blood:	n/a	chr4:48018766-48018779 chr4:48018770-48018783
8	CTCF	chr4:48018180-48018608	HepG2	liver:	n/a	n/a
9	FOXA2	chr4:48018156-48018466	HepG2	liver:	n/a	n/a
10	STAT5A	chr4:48018104-48018656	GM12878	blood:	n/a	chr4:48018112-48018119 chr4:48018481-48018501 chr4:48018105-48018119
11	CTCF	chr4:48018126-48018765	K562	blood:	n/a	n/a
12	CTCF	chr4:48017913-48019455	SK-N-SH	brain:	n/a	n/a
13	FOXA1	chr4:48017703-48018538	HepG2	liver:	n/a	n/a
14	HDAC2	chr4:48018115-48018973	HepG2	liver:	n/a	n/a
15	CTCF	chr4:48018130-48018777	MCF-7	breast:	n/a	n/a
16	REST	chr4:48018146-48019722	H1-neurons	neurons:	n/a	chr4:48018731-48018744 chr4:48018257-48018266 chr4:48018524-48018531
17	MAX	chr4:48018186-48018923	A549	lung:	n/a	n/a
18	RAD21	chr4:48018210-48018590	MCF-7	breast:	n/a	chr4:48018447-48018466
19	ELF1	chr4:48018147-48019831	GM12878	blood:	n/a	n/a
20	FOXA1	chr4:48018147-48018536	HepG2	liver:	n/a	n/a
21	CTCF	chr4:48018138-48018807	A549	lung:	n/a	n/a
22	CTCF	chr4:48018056-48018913	HCT-116	colon:	n/a	n/a
23	TCF12	chr4:48018079-48019092	ECC-1	luminal epithelium:	n/a	chr4:48018588-48018598
24	CTCF	chr4:48018147-48018671	MCF-7	breast:	n/a	n/a
25	MXI1	chr4:48018104-48018957	HepG2	liver:	n/a	n/a
26	FOSL2	chr4:48018229-48018927	HepG2	liver:	n/a	chr4:48018779-48018788
27	HNF4G	chr4:48018102-48018495	HepG2	liver:	n/a	chr4:48018287-48018302 chr4:48018287-48018302 chr4:48018285-48018300 chr4:48018287-48018302 chr4:48018287-48018301
28	NFIC	chr4:48018082-48019067	GM12878	blood:	n/a	n/a
29	TBL1XR1	chr4:48018189-48018248	K562	blood:	n/a	n/a
30	CTCF	chr4:48018190-48018623	H1-hESC	embryonic stem cell:	n/a	n/a
31	RAD21	chr4:48018163-48018649	H1-hESC	embryonic stem cell:	n/a	chr4:48018447-48018466
32	CTCF	chr4:48018184-48018597	K562	blood:	n/a	n/a
33	ZEB1	chr4:48018227-48019203	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:48018149-48019426	H1-hESC	embryonic stem cell:	n/a	n/a
35	REST	chr4:48018154-48018878	HepG2	liver:	n/a	chr4:48018731-48018744 chr4:48018257-48018266 chr4:48018524-48018531
36	HNF4A	chr4:48018132-48018424	HepG2	liver:	n/a	chr4:48018287-48018302 chr4:48018287-48018302 chr4:48018286-48018301 chr4:48018287-48018302 chr4:48018287-48018301
37	HA-E2F1	chr4:48018178-48019571	MCF-7	breast:	n/a	chr4:48018748-48018762 chr4:48018778-48018787 chr4:48018739-48018748
38	MYBL2	chr4:48018138-48018764	HepG2	liver:	n/a	n/a
39	PML	chr4:48018104-48019724	GM12878	blood:	n/a	n/a
40	FOXA1	chr4:48018099-48018927	HepG2	liver:	n/a	n/a
41	CTCF	chr4:48018200-48018350	HVMF	connective:	n/a	n/a
42	JUN	chr4:48018089-48019548	K562	blood:	n/a	chr4:48018779-48018788 chr4:48019256-48019267 chr4:48019253-48019264
43	CTCF	chr4:48018228-48018612	HepG2	liver:	n/a	n/a
44	HNF4A	chr4:48018131-48018458	HepG2	liver:	n/a	chr4:48018287-48018302 chr4:48018287-48018302 chr4:48018286-48018301 chr4:48018287-48018302 chr4:48018287-48018301
45	RUNX3	chr4:48018211-48019351	GM12878	blood:	n/a	n/a
46	ZEB1	chr4:48017689-48019513	HepG2	liver:	n/a	n/a
47	KAP1	chr4:48018033-48019485	HEK293	kidney:	n/a	n/a
48	SIN3A	chr4:48018046-48019563	H1-hESC	embryonic stem cell:	n/a	chr4:48018690-48018699
49	HEY1	chr4:48018177-48019056	HepG2	liver:	n/a	n/a
50	RUNX3	chr4:48018204-48019406	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:47915045..47916605-chr4:48017433..48018940,2	MCF-7	breast:
2	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:
3	chr4:48018226..48018849-chr5:157285675..157286547,2	HCT-116	colon:
4	chr4:48015687..48018286-chr4:48032689..48034980,2	K562	blood:

Variant related genes	Relation type
NIPAL1	TF binding region
CNGA1	TF binding region
ENSG00000163293	Chromatin interaction
ENSG00000113282	Chromatin interaction
ENSG00000170448	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]
rs321630	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
rs321631	NIPAL1	cis	lung	GTEx
rs321631	CNGA1	cis	Esophagus Muscularis	GTEx
rs321631	JPH1	trans	cerebellum	SCAN
rs321631	CNGA1	cis	Heart Left Ventricle	GTEx
rs321631	CNGA1	cis	Artery Aorta	GTEx
rs321631	NFXL1	cis	parietal	SCAN
rs321631	CNGA1	cis	Muscle Skeletal	GTEx
rs321631	CNGA1	cis	Adipose Subcutaneous	GTEx
rs321631	CNGA1	cis	Thyroid	GTEx
rs321631	CNGA1	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48017400-48019200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:48017400-48020200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:48017600-48018400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr4:48017600-48018400	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr4:48017600-48018400	Flanking Active TSS	Stomach Mucosa	stomach
6	chr4:48017600-48019000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:48017600-48019000	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr4:48017600-48019200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:48017600-48020600	Active TSS	Rectal Smooth Muscle	rectum
10	chr4:48017800-48018400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr4:48017800-48018600	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr4:48017800-48018800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:48017800-48019000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:48017800-48019200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:48017800-48019600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr4:48017800-48019800	Active TSS	Esophagus	oesophagus
17	chr4:48017800-48019800	Active TSS	Fetal Kidney	kidney
18	chr4:48018000-48018400	Flanking Active TSS	Hela-S3	cervix
19	chr4:48018000-48018400	Flanking Active TSS	K562	blood
20	chr4:48018000-48018400	Flanking Active TSS	NHEK	skin
21	chr4:48018000-48018600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr4:48018000-48018600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:48018000-48018600	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr4:48018000-48018600	Active TSS	HepG2	liver
25	chr4:48018000-48018600	Flanking Active TSS	HMEC	breast
26	chr4:48018000-48018800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:48018000-48018800	Active TSS	Fetal Intestine Small	intestine
28	chr4:48018000-48019000	Active TSS	H1 Cell Line	embryonic stem cell
29	chr4:48018000-48019000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr4:48018000-48019400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr4:48018000-48019400	Active TSS	Fetal Heart	heart
32	chr4:48018000-48019400	Active TSS	A549	lung
33	chr4:48018000-48019600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:48018000-48019600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:48018000-48019600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:48018000-48019600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
38	chr4:48018000-48019600	Active TSS	Brain Substantia Nigra	brain
39	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr4:48018000-48019800	Active TSS	H9 Cell Line	embryonic stem cell
42	chr4:48018000-48019800	Active TSS	NH-A	brain
43	chr4:48018000-48020000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:48018000-48020400	Active TSS	Duodenum Mucosa	Duodenum
45	chr4:48018000-48020600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:48018200-48018400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr4:48018200-48018400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:48018200-48018400	Active TSS	Primary hematopoietic stem cells	blood
49	chr4:48018200-48018400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr4:48018200-48018400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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