Variant report

Variant	rs5998014
Chromosome Location	chr22:31892438-31892439
allele	G/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	FOXP2	chr22:31892253-31892709	PFSK-1	brain:	n/a	n/a
2	CTCF	chr22:31892300-31892450	HA-sp	spinal cord:	n/a	n/a
3	BCLAF1	chr22:31891896-31892711	GM12878	blood:	n/a	chr22:31892187-31892200 chr22:31892122-31892131 chr22:31892191-31892204
4	POLR2A	chr22:31891857-31893265	GM12892	blood:	n/a	n/a
5	POLR2A	chr22:31891980-31892848	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr22:31892300-31892450	HPF	lung:	n/a	n/a
7	PML	chr22:31891962-31892565	GM12878	blood:	n/a	n/a
8	CTCF	chr22:31892300-31892450	HBMEC	blood vessel:	n/a	n/a
9	RUNX3	chr22:31891860-31894008	GM12878	blood:	n/a	n/a
10	HCFC1	chr22:31891851-31892646	K562	blood:	n/a	n/a
11	NRF1	chr22:31892312-31892530	HepG2	liver:	n/a	chr22:31892409-31892420
12	CBX3	chr22:31892187-31892606	K562	blood:	n/a	n/a
13	GTF2F1	chr22:31892023-31892655	Hela-S3	cervix:	n/a	chr22:31892246-31892257
14	MAZ	chr22:31891683-31892958	GM12878	blood:	n/a	chr22:31891799-31891810 chr22:31891799-31891810
15	ELF1	chr22:31891941-31892585	K562	blood:	n/a	chr22:31892120-31892131
16	FOXM1	chr22:31891888-31892932	GM12878	blood:	n/a	n/a
17	HA-E2F1	chr22:31891997-31893145	MCF-7	breast:	n/a	chr22:31892506-31892517 chr22:31892849-31892861
18	EP300	chr22:31892329-31892569	HepG2	liver:	n/a	n/a
19	CTCF	chr22:31892340-31892490	GM12878	blood:	n/a	n/a
20	TBP	chr22:31891781-31892634	Hela-S3	cervix:	n/a	chr22:31892246-31892257
21	POLR2A	chr22:31891653-31892770	MCF10A-Er-Src	breast:	n/a	n/a
22	TAF1	chr22:31892219-31892790	MCF-7	breast:	n/a	n/a
23	USF1	chr22:31892324-31892572	SK-N-SH_RA	brain:	n/a	n/a
24	GABPA	chr22:31892219-31892845	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr22:31891849-31892856	HepG2	liver:	n/a	n/a
26	POLR2A	chr22:31891843-31892865	HL-60	blood:	n/a	n/a
27	POLR2A	chr22:31892437-31892778	GM12891	blood:	n/a	n/a
28	TCF12	chr22:31891894-31892874	A549	lung:	n/a	chr22:31891971-31891979
29	POLR2A	chr22:31891899-31893258	GM12892	blood:	n/a	n/a
30	POU2F2	chr22:31891948-31892471	GM12891	blood:	n/a	n/a
31	E2F4	chr22:31892254-31892673	GM12878	blood:	n/a	n/a
32	CTCF	chr22:31892238-31892516	SK-N-SH_RA	brain:	n/a	n/a
33	TCF12	chr22:31891884-31892646	ECC-1	luminal epithelium:	n/a	chr22:31891971-31891979
34	POLR2A	chr22:31891963-31892725	A549	lung:	n/a	n/a
35	ZBTB33	chr22:31892268-31892704	K562	blood:	n/a	chr22:31892480-31892495
36	CTCF	chr22:31892320-31892470	A549	lung:	n/a	n/a
37	SIN3AK20	chr22:31891909-31892816	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr22:31891935-31892746	HUVEC	blood vessel:	n/a	n/a
39	CTCF	chr22:31892300-31892450	HMF	breast:	n/a	n/a
40	TAF1	chr22:31892061-31892847	H1-neurons	neurons:	n/a	n/a
41	RUNX3	chr22:31891878-31893271	GM12878	blood:	n/a	n/a
42	CEBPB	chr22:31891827-31892782	GM12878	blood:	n/a	n/a
43	GABPA	chr22:31891863-31893094	MCF-7	breast:	n/a	chr22:31892195-31892204
44	CTCF	chr22:31892360-31892510	GM12865	blood:	n/a	n/a
45	CTCF	chr22:31892340-31892490	AG09319	gingival:	n/a	n/a
46	POU2F2	chr22:31891951-31892483	GM12878	blood:	n/a	n/a
47	CTCF	chr22:31892300-31892450	SK-N-SH_RA	brain:	n/a	n/a
48	CTCF	chr22:31892269-31892476	K562	blood:	n/a	n/a
49	SP1	chr22:31891916-31892490	GM12878	blood:	n/a	chr22:31892339-31892349 chr22:31892433-31892442 chr22:31892433-31892442 chr22:31892432-31892441
50	CTCF	chr22:31892293-31892499	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31891360..31893218-chr22:32058204..32060412,2	MCF-7	breast:
2	chr22:31890586..31892478-chr6:26238591..26241305,2	MCF-7	breast:
3	chr22:31849740..31852347-chr22:31891078..31892965,2	K562	blood:
4	chr11:18416054..18416559-chr22:31892154..31892989,2	Hela-S3	cervix:

Variant related genes	Relation type
SFI1	TF binding region
EIF4ENIF1	TF binding region
ENSG00000241878	Chromatin interaction
ENSG00000198327	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000240591	Chromatin interaction
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12160114	1.00[AFR][1000 genomes]
rs5994385	1.00[AFR][1000 genomes]
rs5994400	1.00[AFR][1000 genomes]
rs5997927	1.00[AFR][1000 genomes]
rs5997931	1.00[AFR][1000 genomes]
rs5998000	1.00[AFR][1000 genomes]
rs5998005	1.00[AFR][1000 genomes]
rs5998020	1.00[AFR][1000 genomes]
rs8143064	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1060776	chr22:31869892-31900359	Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3334530	chr22:31889221-31909085	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31891200-31893200	Active TSS	K562	blood
2	chr22:31891400-31893000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:31891400-31893000	Active TSS	Brain Angular Gyrus	brain
4	chr22:31891400-31893000	Active TSS	Brain Anterior Caudate	brain
5	chr22:31891400-31893000	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr22:31891400-31893200	Active TSS	NHEK	skin
7	chr22:31891400-31893400	Active TSS	Hela-S3	cervix
8	chr22:31891600-31892600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr22:31891600-31892600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr22:31891600-31892800	Active TSS	Right Ventricle	heart
11	chr22:31891600-31892800	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr22:31891600-31892800	Active TSS	Stomach Smooth Muscle	stomach
13	chr22:31891600-31893000	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr22:31891600-31893000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr22:31891600-31893000	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr22:31891600-31893000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr22:31891600-31893000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr22:31891600-31893000	Active TSS	Fetal Brain Female	brain
19	chr22:31891600-31893000	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr22:31891600-31893000	Active TSS	Rectal Smooth Muscle	rectum
21	chr22:31891600-31893200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr22:31891600-31893200	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr22:31891600-31893200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr22:31891600-31893200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr22:31891600-31893200	Active TSS	Fetal Intestine Small	intestine
26	chr22:31891600-31893200	Active TSS	HSMMtube	muscle
27	chr22:31891600-31893400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr22:31891600-31893400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr22:31891600-31893400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr22:31891600-31893400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr22:31891600-31893400	Active TSS	Thymus	Thymus
32	chr22:31891600-31893400	Active TSS	HSMM	muscle
33	chr22:31891600-31893600	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr22:31891600-31893600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr22:31891600-31893600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr22:31891600-31893600	Active TSS	A549	lung
37	chr22:31891600-31893600	Active TSS	NHDF-Ad	bronchial
38	chr22:31891600-31893600	Active TSS	NHLF	lung
39	chr22:31891600-31893600	Active TSS	Osteobl	bone
40	chr22:31891600-31893800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr22:31891800-31892800	Active TSS	Duodenum Mucosa	Duodenum
42	chr22:31891800-31893000	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr22:31891800-31893000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr22:31891800-31893000	Active TSS	Aorta	Aorta
45	chr22:31891800-31893000	Active TSS	Brain Cingulate Gyrus	brain
46	chr22:31891800-31893000	Active TSS	Brain Hippocampus Middle	brain
47	chr22:31891800-31893000	Active TSS	Brain Substantia Nigra	brain
48	chr22:31891800-31893000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr22:31891800-31893000	Active TSS	Left Ventricle	heart
50	chr22:31891800-31893000	Active TSS	HMEC	breast

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