Variant report

Variant	rs4427122
Chromosome Location	chr7:56117707-56117708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:56117687-56123706	K562	blood:	n/a	n/a
2	POLR2A	chr7:56117567-56120230	Raji	blood:	n/a	n/a
3	POLR2A	chr7:56117590-56120711	K562	blood:	n/a	n/a
4	EGR1	chr7:56117597-56117786	K562	blood:	n/a	n/a
5	POLR2A	chr7:56117608-56122645	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr7:56117700-56118540	GM12892	blood:	n/a	n/a
7	POLR2A	chr7:56117595-56120499	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr7:56117587-56119887	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr7:56117175-56121009	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:56117607-56118175	HepG2	liver:	n/a	n/a
11	POLR2A	chr7:56117602-56118563	GM12892	blood:	n/a	n/a
12	POLR2A	chr7:56117697-56122605	GM12891	blood:	n/a	n/a
13	POLR2A	chr7:56117565-56122648	MCF10A-Er-Src	breast:	n/a	n/a
14	ZNF263	chr7:56117693-56118517	HEK293-T-REx	kidney:	n/a	n/a
15	POLR2A	chr7:56117650-56122140	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr7:56117663-56117945	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr7:56117563-56120431	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr7:56117636-56118001	K562	blood:	n/a	n/a
19	UBTF	chr7:56117689-56118530	K562	blood:	n/a	n/a
20	POLR2A	chr7:56117648-56118512	HepG2	liver:	n/a	n/a
21	POLR2A	chr7:56117529-56122526	GM12878	blood:	n/a	n/a
22	MXI1	chr7:56117463-56120735	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:56100362..56103278-chr7:56116659..56119395,4	K562	blood:
2	chr7:56117578..56119708-chr7:56126304..56127920,2	MCF-7	breast:
3	chr7:56029925..56033959-chr7:56116899..56121286,8	MCF-7	breast:
4	chr7:56117123..56123487-chr7:56128716..56133468,11	MCF-7	breast:
5	chr7:56100095..56103801-chr7:56117179..56120388,5	K562	blood:
6	chr7:56031349..56034408-chr7:56116793..56119463,3	K562	blood:

No data

Variant related genes	Relation type
CCT6A	TF binding region
ENSG00000129103	Chromatin interaction
ENSG00000146731	Chromatin interaction
ENSG00000146729	Chromatin interaction
ENSG00000146733	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10265826	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10274148	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12154781	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12155441	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12536548	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12537948	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12668193	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12671494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673255	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13438048	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2014042	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242509	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28438587	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28558245	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778867	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3813505	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4345511	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4424212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4585698	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55940597	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58251663	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59723101	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947671	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6960348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970842	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6971804	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73140779	0.95[AFR][1000 genomes]
rs73140793	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73140794	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs766334	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793536	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7793614	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4427122	SUMF2	cis	Whole Blood	GTEx
rs4427122	SUMF2	cis	lung	GTEx
rs4427122	SUMF2	cis	Artery Tibial	GTEx
rs4427122	SUMF2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56102200-56117800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:56102200-56118200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:56102400-56117800	Weak transcription	Adipose Nuclei	Adipose
4	chr7:56102400-56117800	Weak transcription	Brain Substantia Nigra	brain
5	chr7:56102400-56118000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:56102400-56118000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:56102400-56118000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:56102400-56118000	Weak transcription	Left Ventricle	heart
9	chr7:56102400-56118000	Weak transcription	HSMMtube	muscle
10	chr7:56102400-56118000	Weak transcription	NHLF	lung
11	chr7:56102400-56118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:56102600-56117800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:56102600-56117800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:56102600-56117800	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:56102600-56118000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:56102600-56118000	Weak transcription	Right Atrium	heart
17	chr7:56102800-56118000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:56102800-56118200	Weak transcription	Primary B cells from cord blood	blood
19	chr7:56102800-56118200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:56103000-56118200	Weak transcription	Thymus	Thymus
21	chr7:56107200-56117800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:56108800-56118600	Weak transcription	Aorta	Aorta
23	chr7:56109400-56117800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:56110200-56117800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr7:56110400-56117800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:56110400-56117800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr7:56110400-56118000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:56110400-56118000	Weak transcription	Ovary	ovary
29	chr7:56110600-56117800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr7:56110600-56117800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:56110600-56117800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr7:56110600-56117800	Weak transcription	Placenta	Placenta
33	chr7:56110600-56118000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:56110600-56118200	Weak transcription	Primary T cells from cord blood	blood
35	chr7:56111000-56117800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr7:56111000-56117800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:56111000-56117800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:56111000-56118000	Weak transcription	Fetal Muscle Leg	muscle
39	chr7:56112000-56117800	Weak transcription	NHEK	skin
40	chr7:56112400-56117800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:56112600-56118000	Weak transcription	Brain Angular Gyrus	brain
42	chr7:56113800-56117800	Enhancers	Fetal Intestine Small	intestine
43	chr7:56114000-56118200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:56114600-56118200	Enhancers	Liver	Liver
45	chr7:56115000-56117800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr7:56115400-56117800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:56115400-56117800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr7:56115400-56117800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:56115400-56117800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:56115400-56117800	Weak transcription	Rectal Mucosa Donor 29	rectum

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