Variant report

Variant	rs539283977
Chromosome Location	chr22:29999599-29999600
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	MAX	chr22:29999070-29999989	H1-hESC	embryonic stem cell:	n/a	chr22:29999616-29999627 chr22:29999583-29999592 chr22:29999505-29999515 chr22:29999617-29999626
2	TCF3	chr22:29999565-29999760	GM12878	blood:	n/a	n/a
3	MYC	chr22:29999132-30000233	K562	blood:	n/a	chr22:29999616-29999627 chr22:29999583-29999592 chr22:29999505-29999515 chr22:29999617-29999626
4	CTCF	chr22:29999556-29999700	Fibrobl	skin:	n/a	n/a
5	POLR2A	chr22:29999022-29999853	K562	blood:	n/a	n/a
6	IRF1	chr22:29999026-29999683	K562	blood:	n/a	chr22:29999436-29999445 chr22:29999504-29999518 chr22:29999361-29999368 chr22:29999058-29999065 chr22:29999391-29999405
7	POLR2A	chr22:29999439-30000024	A549	lung:	n/a	n/a
8	HCFC1	chr22:29999218-29999813	K562	blood:	n/a	n/a
9	UBTF	chr22:29999569-30000145	K562	blood:	n/a	n/a
10	POLR2A	chr22:29998973-30000138	GM12878	blood:	n/a	n/a
11	SP2	chr22:29998982-29999673	H1-hESC	embryonic stem cell:	n/a	chr22:29999299-29999322
12	YY1	chr22:29999589-30000114	H1-hESC	embryonic stem cell:	n/a	chr22:29999869-29999883 chr22:29999872-29999886
13	CREB1	chr22:29998930-29999827	GM12878	blood:	n/a	n/a
14	NRF1	chr22:29999318-29999625	K562	blood:	n/a	chr22:29999559-29999568
15	POLR2A	chr22:29998987-30000218	GM12892	blood:	n/a	n/a
16	USF1	chr22:29999461-29999770	H1-hESC	embryonic stem cell:	n/a	chr22:29999508-29999524
17	POLR2A	chr22:29999042-30000157	A549	lung:	n/a	n/a
18	CHD2	chr22:29999128-29999602	H1-hESC	embryonic stem cell:	n/a	chr22:29999200-29999210
19	NR2F2	chr22:29998998-29999809	K562	blood:	n/a	n/a
20	CREB1	chr22:29998991-29999811	GM12878	blood:	n/a	n/a
21	CTCF	chr22:29999597-29999603	MCF-7	breast:	n/a	n/a
22	E2F6	chr22:29999002-30000073	K562	blood:	n/a	chr22:29999012-29999019 chr22:29999406-29999413 chr22:29999012-29999019 chr22:29999402-29999414 chr22:29999008-29999020 chr22:29999406-29999413 chr22:29999521-29999531 chr22:29999012-29999019 chr22:29999225-29999240 chr22:29999406-29999413 chr22:29999436-29999445
23	POLR2A	chr22:29999008-30000228	GM19193	blood:	n/a	n/a
24	JUN	chr22:29998932-30000264	K562	blood:	n/a	n/a
25	MXI1	chr22:29999187-30000381	Hela-S3	cervix:	n/a	n/a
26	CREB1	chr22:29999118-29999842	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr22:29999424-29999734	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr22:29998691-29999990	PFSK-1	brain:	n/a	n/a
29	RELA	chr22:29999097-30000205	GM18951	blood:	n/a	n/a
30	RFX5	chr22:29998820-30000563	SK-N-SH	brain:	n/a	n/a
31	USF2	chr22:29999397-29999777	GM12878	blood:	n/a	chr22:29999508-29999524
32	CTCF	chr22:29999468-29999733	K562	blood:	n/a	n/a
33	POLR2A	chr22:29998949-30000331	GM12892	blood:	n/a	n/a
34	RUNX3	chr22:29999024-29999768	GM12878	blood:	n/a	n/a
35	POLR2A	chr22:29999387-29999794	H1-hESC	embryonic stem cell:	n/a	n/a
36	KAP1	chr22:29999094-29999983	HEK293	kidney:	n/a	n/a
37	USF2	chr22:29999562-29999666	K562	blood:	n/a	n/a
38	SP1	chr22:29999106-29999749	K562	blood:	n/a	chr22:29999391-29999402 chr22:29999504-29999516 chr22:29999391-29999403 chr22:29999506-29999515 chr22:29999505-29999515 chr22:29999505-29999514 chr22:29999501-29999515 chr22:29999504-29999516
39	YY1	chr22:29998968-30000261	GM12878	blood:	n/a	chr22:29999869-29999883 chr22:29999502-29999516 chr22:30000112-30000126 chr22:29999872-29999886
40	POU2F2	chr22:29999027-29999654	GM12878	blood:	n/a	n/a
41	REST	chr22:29999085-30000504	H1-neurons	neurons:	n/a	chr22:29999518-29999531 chr22:30000113-30000126 chr22:29999945-29999958 chr22:29999762-29999775
42	CTCF	chr22:29999500-29999650	AG09319	gingival:	n/a	n/a
43	TAF1	chr22:29999414-29999711	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr22:29999026-30000207	HEK293	kidney:	n/a	n/a
45	MAX	chr22:29999101-30000097	GM12878	blood:	n/a	chr22:29999616-29999627 chr22:29999583-29999592 chr22:29999505-29999515 chr22:29999617-29999626
46	MYC	chr22:29999338-29999725	MCF-7	breast:	n/a	chr22:29999616-29999627 chr22:29999583-29999592 chr22:29999505-29999515 chr22:29999617-29999626
47	CTCF	chr22:29999560-29999710	GM12871	blood:	n/a	n/a
48	TCF12	chr22:29999412-29999708	GM12878	blood:	n/a	n/a
49	TBP	chr22:29999074-29999665	GM12878	blood:	n/a	n/a
50	CTCF	chr22:29999562-29999707	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:29999554-29999604	HCF	heart:	n/a
2	chr22:29999554-29999604	HCM	heart:	n/a
3	chr22:29999554-29999604	HepG2	liver:	n/a
4	chr22:29999554-29999604	SK-N-MC	brain:	n/a
5	chr22:29999554-29999604	AG10803	skin:	n/a
6	chr22:29999554-29999604	NB4	blood:	n/a
7	chr22:29999554-29999604	Caco-2	colon:	n/a
8	chr22:29999554-29999604	BE2_C	brain:	n/a
9	chr22:29999554-29999604	AG04449	skin:	fetal
10	chr22:29999554-29999604	SK-N-SH_RA	brain:	n/a
11	chr22:29999554-29999604	T-47D	breast:	n/a
12	chr22:29999554-29999604	HCPEpiC	choroid plexus:	n/a
13	chr22:29999554-29999604	Jurkat	blood:	n/a
14	chr22:29999554-29999604	CMK	blood:	n/a
15	chr22:29999554-29999604	NHBE	bronchial:	n/a
16	chr22:29999554-29999604	GM12891	blood:	n/a
17	chr22:29999554-29999604	GM06990	blood:	n/a
18	chr22:29999554-29999604	HMEC	breast:	n/a
19	chr22:29999554-29999604	HNPCEpiC	eye:	n/a
20	chr22:29999554-29999604	BJ	skin:	n/a
21	chr22:29999554-29999604	HL-60	blood:	n/a
22	chr22:29999554-29999604	LNCaP	prostate:	n/a
23	chr22:29999554-29999604	Hepatocyte	liver:	n/a
24	chr22:29999554-29999604	SAEC	small airway:	n/a
25	chr22:29999554-29999604	ProgFib	skin:	n/a
26	chr22:29999554-29999604	HIPEpiC	eye:	n/a
27	chr22:29999554-29999604	HRCEpiC	kidney:	n/a
28	chr22:29999554-29999604	SK-N-SH	brain:	n/a
29	chr22:29999554-29999604	ovcar-3	ovarian:	n/a
30	chr22:29999554-29999604	AG09309	skin:	n/a
31	chr22:29999554-29999604	H1-hESC	embryonic stem cell:	embryo
32	chr22:29999554-29999604	AoSMC	blood vessel:	n/a
33	chr22:29999554-29999604	HEK293	kidney:	embryo
34	chr22:29999554-29999604	MCF10A-Er-Src	breast:	n/a
35	chr22:29999554-29999604	NHDF-neo	bronchial:	n/a
36	chr22:29999554-29999604	PrEC	prostate:	n/a
37	chr22:29999554-29999604	GM12892	blood:	n/a
38	chr22:29999554-29999604	HUVEC	blood vessel:	n/a
39	chr22:29999554-29999604	HAEpiC	amniotic membrane:	n/a
40	chr22:29999554-29999604	AG09319	gingival:	n/a
41	chr22:29999554-29999604	U87	brain:	n/a
42	chr22:29999554-29999604	HCT-116	colon:	n/a
43	chr22:29999554-29999604	A549	lung:	n/a
44	chr22:29999554-29999604	NT2-D1	testis:	n/a
45	chr22:29999554-29999604	MCF-7	breast:	n/a
46	chr22:29999554-29999604	HRE	kidney:	n/a
47	chr22:29999554-29999604	RPTEC	kidney:	n/a
48	chr22:29999554-29999604	GM19239	blood:	n/a
49	chr22:29999554-29999604	NH-A	brain:	n/a
50	chr22:29999554-29999604	HRPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:52026823..52027558-chr22:29999049..30000022,2	HCT-116	colon:
2	chr22:29975483..29978642-chr22:29996311..30000725,6	MCF-7	breast:
3	chr22:29999342..30001478-chr22:30003978..30005588,2	MCF-7	breast:
4	chr22:29998884..29999633-chr3:23958298..23958926,2	NB4	blood:
5	chr22:29975560..29978145-chr22:29998416..30001350,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEFH-1	chr22:29999564-29999811	NONHSAT084713
2	lnc-NEFH-1	chr22:29999564-29999796	NONHSAT084714

Variant related genes	Relation type
NF2	TF binding region
NF2	CpG island
ENSG00000236778	Chromatin interaction
ENSG00000184117	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000233010	Chromatin interaction
ENSG00000174748	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
9	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29998400-30000200	Active TSS	Primary T killer memory cells from peripheral blood	blood
2	chr22:29998400-30001200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr22:29998600-30000000	Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr22:29998600-30000400	Active TSS	Brain Cingulate Gyrus	brain
5	chr22:29998600-30000600	Active TSS	Hela-S3	cervix
6	chr22:29998600-30000800	Active TSS	Colonic Mucosa	Colon
7	chr22:29998600-30001400	Active TSS	GM12878-XiMat	blood
8	chr22:29998600-30002000	Active TSS	HSMM	muscle
9	chr22:29998800-30000000	Active TSS	Stomach Smooth Muscle	stomach
10	chr22:29998800-30000000	Active TSS	Monocytes-CD14+_RO01746	blood
11	chr22:29998800-30000200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr22:29998800-30000400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr22:29998800-30000400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:29998800-30000400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr22:29998800-30000400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr22:29998800-30000400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr22:29998800-30000400	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr22:29998800-30000400	Active TSS	Dnd41	blood
19	chr22:29998800-30000800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:29998800-30001000	Active TSS	Right Atrium	heart
21	chr22:29998800-30001000	Active TSS	Thymus	Thymus
22	chr22:29998800-30001200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr22:29998800-30001200	Active TSS	Right Ventricle	heart
24	chr22:29999000-29999800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr22:29999000-29999800	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr22:29999000-30000000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr22:29999000-30000000	Active TSS	Primary hematopoietic stem cells	blood
28	chr22:29999000-30000000	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr22:29999000-30000000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr22:29999000-30000000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr22:29999000-30000000	Active TSS	Adipose Nuclei	Adipose
32	chr22:29999000-30000000	Active TSS	Placenta Amnion	Placenta Amnion
33	chr22:29999000-30000200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr22:29999000-30000200	Active TSS	Liver	Liver
35	chr22:29999000-30000200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr22:29999000-30000200	Active TSS	Fetal Intestine Large	intestine
37	chr22:29999000-30000200	Active TSS	Rectal Smooth Muscle	rectum
38	chr22:29999000-30000200	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr22:29999000-30000200	Active TSS	Stomach Mucosa	stomach
40	chr22:29999000-30000200	Active TSS	Osteobl	bone
41	chr22:29999000-30000400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr22:29999000-30000400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr22:29999000-30000400	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr22:29999000-30000400	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr22:29999000-30000400	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr22:29999000-30000400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr22:29999000-30000400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr22:29999000-30000400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr22:29999000-30000400	Active TSS	Brain Angular Gyrus	brain
50	chr22:29999000-30000400	Active TSS	Brain Anterior Caudate	brain

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