Variant report

Variant	rs2622917
Chromosome Location	chr1:47902286-47902287
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	chr1:47901943-47902736	HCT-116	colon:	n/a	chr1:47902581-47902591 chr1:47902581-47902593
2	RAD21	chr1:47902125-47902523	SK-N-SH_RA	brain:	n/a	n/a
3	ZEB1	chr1:47902190-47902452	GM12878	blood:	n/a	n/a
4	MTA3	chr1:47901994-47902922	GM12878	blood:	n/a	n/a
5	MXI1	chr1:47902143-47902673	HepG2	liver:	n/a	chr1:47902655-47902670
6	CTCF	chr1:47902119-47902522	GM19238	blood:	n/a	n/a
7	FOXP2	chr1:47902182-47902450	SK-N-MC	brain:	n/a	n/a
8	CTCF	chr1:47902220-47902370	HEK293	kidney:	n/a	n/a
9	USF2	chr1:47902125-47902446	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:47902127-47903588	GM12878	blood:	n/a	n/a
11	RAD21	chr1:47901998-47902598	ECC-1	luminal epithelium:	n/a	chr1:47902581-47902591 chr1:47902581-47902593
12	CTCF	chr1:47901969-47903966	A549	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
13	RAD21	chr1:47902110-47902546	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr1:47902153-47902534	A549	lung:	n/a	n/a
15	RAD21	chr1:47902140-47902501	HepG2	liver:	n/a	n/a
16	CTCF	chr1:47902220-47902370	WI-38	lung:	n/a	n/a
17	CTCF	chr1:47902083-47903846	IMR90	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
18	TCF7L2	chr1:47902190-47903850	HCT-116	colon:	n/a	n/a
19	ELF1	chr1:47902073-47903938	K562	blood:	n/a	chr1:47903423-47903436 chr1:47903588-47903600 chr1:47903133-47903145 chr1:47903288-47903300 chr1:47903322-47903331 chr1:47903787-47903796 chr1:47903785-47903797 chr1:47903292-47903301 chr1:47903793-47903802 chr1:47903655-47903667 chr1:47903784-47903793 chr1:47903788-47903800 chr1:47903315-47903327
20	ELF1	chr1:47902132-47902414	HepG2	liver:	n/a	n/a
21	CREB1	chr1:47902163-47902445	A549	lung:	n/a	n/a
22	RCOR1	chr1:47901790-47903838	K562	blood:	n/a	n/a
23	CTCF	chr1:47902200-47902350	HVMF	connective:	n/a	n/a
24	CTCF	chr1:47902044-47902545	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr1:47902220-47902370	K562	blood:	n/a	n/a
26	YY1	chr1:47902053-47902463	GM12878	blood:	n/a	n/a
27	CTCF	chr1:47902180-47902330	HCM	heart:	n/a	n/a
28	FOXM1	chr1:47902048-47902487	GM12878	blood:	n/a	n/a
29	UBTF	chr1:47902126-47904027	K562	blood:	n/a	n/a
30	BHLHE40	chr1:47902112-47902522	GM12878	blood:	n/a	n/a
31	CTCF	chr1:47902220-47902370	HBMEC	blood vessel:	n/a	n/a
32	ZBTB7A	chr1:47902143-47904182	K562	blood:	n/a	chr1:47903645-47903654
33	TEAD4	chr1:47902058-47902596	K562	blood:	n/a	n/a
34	CTCFL	chr1:47902190-47902363	K562	blood:	n/a	n/a
35	CTCF	chr1:47902220-47902370	AG04449	skin:	n/a	n/a
36	CTCF	chr1:47902170-47902432	LNCaP	prostate:	n/a	n/a
37	CTCF	chr1:47902220-47902370	GM12868	blood:	n/a	n/a
38	TCF12	chr1:47902159-47902373	GM12878	blood:	n/a	chr1:47902311-47902321
39	CTCF	chr1:47902160-47902310	HAc	cerebellar:	n/a	n/a
40	MAX	chr1:47902072-47903880	NB4	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
41	NR2F2	chr1:47902020-47902814	K562	blood:	n/a	n/a
42	ZNF384	chr1:47901817-47902461	GM12878	blood:	n/a	n/a
43	MYC	chr1:47902219-47902425	MCF10A-Er-Src	breast:	n/a	n/a
44	CTCF	chr1:47902220-47902370	GM12873	blood:	n/a	n/a
45	CTCF	chr1:47902200-47902350	MCF-7	breast:	n/a	n/a
46	POLR2A	chr1:47902034-47904062	HEK293	kidney:	n/a	n/a
47	STAT5A	chr1:47901959-47902550	GM12878	blood:	n/a	n/a
48	CTCF	chr1:47902130-47902462	MCF-7	breast:	n/a	n/a
49	CTCF	chr1:47902220-47902370	Caco-2	colon:	n/a	n/a
50	CTCF	chr1:47902240-47902390	HUVEC	blood vessel:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:47902269-47902319	GM12878	blood:	n/a
2	chr1:47902269-47902319	ProgFib	skin:	n/a
3	chr1:47902275-47902325	HEK293	kidney:	embryo
4	chr1:47902275-47902325	GM12878	blood:	n/a
5	chr1:47902269-47902319	Jurkat	blood:	n/a
6	chr1:47902269-47902319	Hepatocyte	liver:	n/a
7	chr1:47902275-47902325	RPTEC	kidney:	n/a
8	chr1:47902275-47902325	HUVEC	blood vessel:	n/a
9	chr1:47902269-47902319	PFSK-1	brain:	n/a
10	chr1:47902275-47902325	HRCEpiC	kidney:	n/a
11	chr1:47902275-47902325	AG10803	skin:	n/a
12	chr1:47902269-47902319	SK-N-MC	brain:	n/a
13	chr1:47902269-47902319	RPTEC	kidney:	n/a
14	chr1:47902275-47902325	ProgFib	skin:	n/a
15	chr1:47902269-47902319	SKMC	muscle:	n/a
16	chr1:47902269-47902319	HRCEpiC	kidney:	n/a
17	chr1:47902275-47902325	AG09309	skin:	n/a
18	chr1:47902275-47902325	LNCaP	prostate:	n/a
19	chr1:47902275-47902325	BJ	skin:	n/a
20	chr1:47902269-47902319	SK-N-SH	brain:	n/a
21	chr1:47902275-47902325	ovcar-3	ovarian:	n/a
22	chr1:47902275-47902325	HCM	heart:	n/a
23	chr1:47902275-47902325	NH-A	brain:	n/a
24	chr1:47902269-47902319	BE2_C	brain:	n/a
25	chr1:47902275-47902325	HEEpiC	esophagus:	n/a
26	chr1:47902269-47902319	NHDF-neo	bronchial:	n/a
27	chr1:47902269-47902319	IMR90	lung:	fetal
28	chr1:47902269-47902319	U87	brain:	n/a
29	chr1:47902269-47902319	HCM	heart:	n/a
30	chr1:47902269-47902319	HAEpiC	amniotic membrane:	n/a
31	chr1:47902275-47902325	GM19239	blood:	n/a
32	chr1:47902269-47902319	HEK293	kidney:	embryo
33	chr1:47902275-47902325	U87	brain:	n/a
34	chr1:47902269-47902319	NT2-D1	testis:	n/a
35	chr1:47902275-47902325	ECC-1	luminal epithelium:	n/a
36	chr1:47902269-47902319	ovcar-3	ovarian:	n/a
37	chr1:47902269-47902319	HIPEpiC	eye:	n/a
38	chr1:47902269-47902319	HCT-116	colon:	n/a
39	chr1:47902269-47902319	HEEpiC	esophagus:	n/a
40	chr1:47902269-47902319	MCF10A-Er-Src	breast:	n/a
41	chr1:47902275-47902325	NHBE	bronchial:	n/a
42	chr1:47902275-47902325	H1-hESC	embryonic stem cell:	embryo
43	chr1:47902269-47902319	HMEC	breast:	n/a
44	chr1:47902275-47902325	PFSK-1	brain:	n/a
45	chr1:47902269-47902319	HNPCEpiC	eye:	n/a
46	chr1:47902269-47902319	PrEC	prostate:	n/a
47	chr1:47902275-47902325	GM12892	blood:	n/a
48	chr1:47902275-47902325	SK-N-SH_RA	brain:	n/a
49	chr1:47902269-47902319	T-47D	breast:	n/a
50	chr1:47902269-47902319	HUVEC	blood vessel:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47901774..47903783-chr1:47905502..47907193,2	MCF-7	breast:
2	chr1:47901790..47903824-chr1:48190200..48191775,2	K562	blood:
3	chr1:47902132..47902815-chr1:48175858..48176824,3	MCF-7	breast:
4	chr1:47902221..47904815-chr1:47929260..47931018,2	K562	blood:
5	chr1:47901999..47903599-chr1:48174794..48176429,2	MCF-7	breast:
6	chr1:47901910..47902768-chr1:48089857..48090558,2	K562	blood:
7	chr1:47901811..47902631-chr1:47910399..47911268,2	K562	blood:
8	chr1:47902027..47902996-chr1:47935255..47935856,2	K562	blood:
9	chr1:47901842..47902786-chr1:48175848..48176467,3	K562	blood:

Variant related genes	Relation type
FOXD2-AS1	TF binding region
FOXD2-AS1	CpG island

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10399673	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12070024	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12090153	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1316443	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1680020	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2405922	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622909	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2622920	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622921	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2820970	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2820971	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2820974	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738315	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4603175	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs505399	0.80[AMR][1000 genomes]
rs524158	0.80[AMR][1000 genomes]
rs527551	0.83[AMR][1000 genomes]
rs538286	0.80[AMR][1000 genomes]
rs55718554	0.87[EUR][1000 genomes]
rs557851	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs571281	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61103903	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6673882	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6673934	0.85[EUR][1000 genomes]
rs7552140	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436899	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3432093	chr1:47901465-47906063	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv3406880	chr1:47901890-47905238	Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2622917	CMPK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47899000-47904400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:47901400-47902400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
3	chr1:47901400-47902800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr1:47901400-47908000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
5	chr1:47901600-47902600	Flanking Active TSS	GM12878-XiMat	blood
6	chr1:47901600-47902800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr1:47901600-47902800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
8	chr1:47901800-47902400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:47901800-47902400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:47901800-47902400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:47901800-47902400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
12	chr1:47901800-47902400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
13	chr1:47901800-47902400	Bivalent Enhancer	Fetal Lung	lung
14	chr1:47901800-47902400	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr1:47901800-47902400	Bivalent Enhancer	Fetal Stomach	stomach
16	chr1:47901800-47902600	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr1:47901800-47902800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:47901800-47902800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:47901800-47902800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
20	chr1:47901800-47903200	Flanking Active TSS	Liver	Liver
21	chr1:47901800-47903200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr1:47901800-47904000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
23	chr1:47901800-47904600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:47902000-47902400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
25	chr1:47902000-47902400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
26	chr1:47902000-47902400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
27	chr1:47902000-47902400	Enhancers	Primary B cells from peripheral blood	blood
28	chr1:47902000-47902400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:47902000-47902400	Bivalent Enhancer	Placenta	Placenta
30	chr1:47902000-47902400	Flanking Active TSS	Dnd41	blood
31	chr1:47902000-47902400	Enhancers	HSMMtube	muscle
32	chr1:47902000-47902400	Flanking Active TSS	Osteobl	bone
33	chr1:47902000-47902600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:47902000-47902600	Bivalent/Poised TSS	Psoas Muscle	Psoas
35	chr1:47902000-47902800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:47902000-47902800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:47902000-47902800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:47902000-47902800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:47902000-47902800	Flanking Active TSS	Colonic Mucosa	Colon
40	chr1:47902000-47902800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr1:47902000-47902800	Bivalent Enhancer	Fetal Heart	heart
42	chr1:47902000-47902800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr1:47902000-47902800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
44	chr1:47902000-47903000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr1:47902000-47903000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr1:47902000-47903200	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr1:47902000-47903200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:47902000-47903200	Flanking Active TSS	HUVEC	blood vessel
49	chr1:47902000-47903600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:47902000-47904400	Bivalent/Poised TSS	Brain Anterior Caudate	brain

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