Variant report

Variant	rs321632
Chromosome Location	chr4:48018328-48018329
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	POLR2A	chr4:48018318-48018969	HepG2	liver:	n/a	n/a
2	MAFF	chr4:48018192-48018385	HepG2	liver:	n/a	n/a
3	NR2F2	chr4:48018230-48019080	MCF-7	breast:	n/a	n/a
4	YY1	chr4:48018282-48018528	HCT-116	colon:	n/a	n/a
5	RCOR1	chr4:48018237-48018639	K562	blood:	n/a	n/a
6	E2F6	chr4:48018272-48019360	H1-hESC	embryonic stem cell:	n/a	chr4:48018748-48018762 chr4:48018778-48018787 chr4:48018739-48018748
7	RAD21	chr4:48018175-48018657	HepG2	liver:	n/a	chr4:48018447-48018466
8	STAT5A	chr4:48018321-48018627	GM12878	blood:	n/a	chr4:48018481-48018501
9	RAD21	chr4:48018163-48018609	H1-hESC	embryonic stem cell:	n/a	chr4:48018447-48018466
10	RAD21	chr4:48018300-48018591	K562	blood:	n/a	chr4:48018447-48018466
11	RAD21	chr4:48018175-48018657	ECC-1	luminal epithelium:	n/a	chr4:48018447-48018466
12	TCF12	chr4:48018136-48019597	ECC-1	luminal epithelium:	n/a	chr4:48018588-48018598
13	SETDB1	chr4:48018229-48018666	U2OS	brain:	n/a	n/a
14	POLR2A	chr4:48018308-48018991	GM12878	blood:	n/a	n/a
15	BCLAF1	chr4:48018183-48019163	GM12878	blood:	n/a	chr4:48018766-48018779 chr4:48018770-48018783
16	TFAP2C	chr4:48018288-48019589	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr4:48018320-48018470	HEK293	kidney:	n/a	n/a
18	CTBP2	chr4:48018238-48019635	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAZ	chr4:48018275-48019179	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr4:48018180-48018608	HepG2	liver:	n/a	n/a
21	FOXA2	chr4:48018156-48018466	HepG2	liver:	n/a	n/a
22	STAT5A	chr4:48018104-48018656	GM12878	blood:	n/a	chr4:48018112-48018119 chr4:48018481-48018501 chr4:48018105-48018119
23	CTCF	chr4:48018246-48018590	T-47D	breast:	n/a	n/a
24	CTCF	chr4:48018126-48018765	K562	blood:	n/a	n/a
25	MAX	chr4:48018280-48019499	MCF-7	breast:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
26	CTCF	chr4:48018283-48018618	GM19238	blood:	n/a	n/a
27	TCF7L2	chr4:48018232-48018684	Hela-S3	cervix:	n/a	n/a
28	NFATC1	chr4:48018242-48018640	GM12878	blood:	n/a	n/a
29	CTCF	chr4:48018241-48018653	K562	blood:	n/a	n/a
30	CTCF	chr4:48017913-48019455	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr4:48018322-48018606	ProgFib	skin:	n/a	n/a
32	FOXA1	chr4:48017703-48018538	HepG2	liver:	n/a	n/a
33	POLR2A	chr4:48018327-48019709	ECC-1	luminal epithelium:	n/a	n/a
34	RCOR1	chr4:48018256-48018406	K562	blood:	n/a	n/a
35	RAD21	chr4:48018269-48018696	GM12878	blood:	n/a	chr4:48018447-48018466
36	CTCF	chr4:48018283-48018589	T-47D	breast:	n/a	n/a
37	CTCF	chr4:48018299-48018603	A549	lung:	n/a	n/a
38	HDAC2	chr4:48018115-48018973	HepG2	liver:	n/a	n/a
39	CTCF	chr4:48018130-48018777	MCF-7	breast:	n/a	n/a
40	TBP	chr4:48018240-48019595	H1-hESC	embryonic stem cell:	n/a	n/a
41	REST	chr4:48018146-48019722	H1-neurons	neurons:	n/a	chr4:48018731-48018744 chr4:48018257-48018266 chr4:48018524-48018531
42	HMGN3	chr4:48018289-48018979	K562	blood:	n/a	n/a
43	MAX	chr4:48018186-48018923	A549	lung:	n/a	n/a
44	RAD21	chr4:48018239-48018714	SK-N-SH_RA	brain:	n/a	chr4:48018447-48018466
45	RAD21	chr4:48018210-48018590	MCF-7	breast:	n/a	chr4:48018447-48018466
46	CTCF	chr4:48018305-48018584	SK-N-SH_RA	brain:	n/a	n/a
47	POLR2A	chr4:48018289-48019599	HCT-116	colon:	n/a	n/a
48	ELF1	chr4:48018147-48019831	GM12878	blood:	n/a	n/a
49	FOXA1	chr4:48018147-48018536	HepG2	liver:	n/a	n/a
50	CTCF	chr4:48018138-48018807	A549	lung:	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:

Variant related genes	Relation type
CNGA1	TF binding region
NIPAL1	TF binding region
ENSG00000113282	Chromatin interaction
ENSG00000170448	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10025104	0.80[GIH][hapmap]
rs1003873	0.87[JPT][hapmap]
rs10938516	0.88[YRI][hapmap]
rs13116684	0.81[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13121957	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13145218	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13150783	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13151608	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1348023	0.83[GIH][hapmap]
rs1507922	0.87[GIH][hapmap]
rs1567217	0.93[JPT][hapmap]
rs167692	0.83[GIH][hapmap]
rs2053404	0.80[GIH][hapmap]
rs224799	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279965	0.87[JPT][hapmap]
rs2289433	0.80[GIH][hapmap]
rs321622	0.81[ASW][hapmap]
rs321628	0.81[AFR][1000 genomes]
rs321630	0.88[ASW][hapmap];0.85[LWK][hapmap];0.81[AFR][1000 genomes]
rs321631	0.88[ASW][hapmap];0.85[LWK][hapmap];0.81[AFR][1000 genomes]
rs321634	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321635	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35085584	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4694872	0.80[GIH][hapmap]
rs4695303	0.80[GIH][hapmap]
rs4695306	0.80[GIH][hapmap]
rs4695325	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55670663	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414687	0.80[GIH][hapmap]
rs6447609	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6812991	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6818556	0.80[GIH][hapmap]
rs6841271	0.83[GIH][hapmap]
rs7674929	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9291317	0.80[GIH][hapmap]
rs98270	0.82[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs321632	NFXL1	cis	multi-tissue	Pritchard
rs321632	CNGA1	cis	Thyroid	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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