Variant report

Variant	rs554700762
Chromosome Location	chr22:29875612-29875613
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	MXI1	chr22:29875358-29878062	SK-N-SH	brain:	n/a	chr22:29877653-29877662
2	REST	chr22:29875571-29875784	SK-N-SH	brain:	n/a	n/a
3	REST	chr22:29873719-29876257	ECC-1	luminal epithelium:	n/a	chr22:29874670-29874684 chr22:29876114-29876127 chr22:29874664-29874684 chr22:29876194-29876204 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189 chr22:29876192-29876206
4	REST	chr22:29875494-29875719	K562	blood:	n/a	n/a
5	REST	chr22:29873747-29876490	ECC-1	luminal epithelium:	n/a	chr22:29874670-29874684 chr22:29876114-29876127 chr22:29874664-29874684 chr22:29876194-29876204 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189 chr22:29876192-29876206
6	REST	chr22:29873788-29876008	HL-60	blood:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:29875592-29875642	AG09319	gingival:	n/a
2	chr22:29875578-29875628	MCF10A-Er-Src	breast:	n/a
3	chr22:29875578-29875628	HPAEpiC	pulmonary alveolar:	n/a
4	chr22:29875578-29875628	AG10803	skin:	n/a
5	chr22:29875578-29875628	HCF	heart:	n/a
6	chr22:29875592-29875642	CMK	blood:	n/a
7	chr22:29875592-29875642	SK-N-SH_RA	brain:	n/a
8	chr22:29875592-29875642	Hela-S3	cervix:	n/a
9	chr22:29875592-29875642	HCPEpiC	choroid plexus:	n/a
10	chr22:29875592-29875642	GM12891	blood:	n/a
11	chr22:29875578-29875628	K562	blood:	n/a
12	chr22:29875592-29875642	MCF10A-Er-Src	breast:	n/a
13	chr22:29875592-29875642	SK-N-SH	brain:	n/a
14	chr22:29875578-29875628	A549	lung:	n/a
15	chr22:29875592-29875642	PrEC	prostate:	n/a
16	chr22:29875592-29875642	HRPEpiC	eye:	n/a
17	chr22:29875578-29875628	ovcar-3	ovarian:	n/a
18	chr22:29875578-29875628	PFSK-1	brain:	n/a
19	chr22:29875592-29875642	HIPEpiC	eye:	n/a
20	chr22:29875592-29875642	AG10803	skin:	n/a
21	chr22:29875592-29875642	SKMC	muscle:	n/a
22	chr22:29875592-29875642	ECC-1	luminal epithelium:	n/a
23	chr22:29875578-29875628	AG09319	gingival:	n/a
24	chr22:29875592-29875642	HCT-116	colon:	n/a
25	chr22:29875592-29875642	PFSK-1	brain:	n/a
26	chr22:29875592-29875642	GM12878	blood:	n/a
27	chr22:29875592-29875642	GM19239	blood:	n/a
28	chr22:29875578-29875628	GM12892	blood:	n/a
29	chr22:29875578-29875628	HCPEpiC	choroid plexus:	n/a
30	chr22:29875578-29875628	AoSMC	blood vessel:	n/a
31	chr22:29875592-29875642	NHDF-neo	bronchial:	n/a
32	chr22:29875578-29875628	HRE	kidney:	n/a
33	chr22:29875578-29875628	Hela-S3	cervix:	n/a
34	chr22:29875578-29875628	HL-60	blood:	n/a
35	chr22:29875578-29875628	HNPCEpiC	eye:	n/a
36	chr22:29875592-29875642	BJ	skin:	n/a
37	chr22:29875592-29875642	Hepatocyte	liver:	n/a
38	chr22:29875592-29875642	T-47D	breast:	n/a
39	chr22:29875592-29875642	MCF-7	breast:	n/a
40	chr22:29875592-29875642	HRE	kidney:	n/a
41	chr22:29875592-29875642	GM06990	blood:	n/a
42	chr22:29875592-29875642	ProgFib	skin:	n/a
43	chr22:29875592-29875642	Jurkat	blood:	n/a
44	chr22:29875578-29875628	BE2_C	brain:	n/a
45	chr22:29875578-29875628	HCT-116	colon:	n/a
46	chr22:29875578-29875628	RPTEC	kidney:	n/a
47	chr22:29875592-29875642	NT2-D1	testis:	n/a
48	chr22:29875578-29875628	HepG2	liver:	n/a
49	chr22:29875578-29875628	HAEpiC	amniotic membrane:	n/a
50	chr22:29875592-29875642	NHBE	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29783197..29785326-chr22:29874558..29877420,2	MCF-7	breast:
2	chr22:29702481..29704174-chr22:29874105..29876353,2	K562	blood:
3	chr22:29873715..29877046-chr22:29940798..29944268,3	K562	blood:

Variant related genes	Relation type
NEFH	TF binding region
RFPL1S	TF binding region
NEFH	CpG island
RFPL1S	CpG island
ENSG00000185340	Chromatin interaction
ENSG00000100296	Chromatin interaction
ENSG00000100280	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv1062039	chr22:29854861-29889201	Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv438344	chr22:29856079-29886043	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3371117	chr22:29874452-29879050	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29873400-29875800	Enhancers	K562	blood
2	chr22:29873800-29875800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
3	chr22:29873800-29876200	Bivalent Enhancer	Adipose Nuclei	Adipose
4	chr22:29873800-29876400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
5	chr22:29873800-29877800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
6	chr22:29873800-29877800	Bivalent Enhancer	Placenta	Placenta
7	chr22:29874000-29876200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:29874200-29875800	Enhancers	Ovary	ovary
9	chr22:29874200-29876000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr22:29874200-29876400	Bivalent Enhancer	Fetal Stomach	stomach
11	chr22:29874400-29877000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr22:29874400-29877600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr22:29874400-29877600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr22:29874600-29875800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr22:29874600-29876000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
16	chr22:29874600-29876400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr22:29874600-29877400	Active TSS	Brain Anterior Caudate	brain
18	chr22:29874600-29878000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
19	chr22:29874800-29875800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
20	chr22:29874800-29876200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
21	chr22:29874800-29876400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr22:29874800-29876400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
23	chr22:29874800-29877800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
24	chr22:29875000-29876000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr22:29875000-29876000	Weak transcription	Gastric	stomach
26	chr22:29875000-29878000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
27	chr22:29875200-29875800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr22:29875200-29876000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr22:29875200-29876000	Bivalent Enhancer	Spleen	Spleen
30	chr22:29875200-29877600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr22:29875400-29875800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr22:29875400-29875800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr22:29875400-29876000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
34	chr22:29875400-29876000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
35	chr22:29875400-29876000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
36	chr22:29875400-29876200	Bivalent/Poised TSS	Right Ventricle	heart
37	chr22:29875400-29876400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
38	chr22:29875400-29876800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr22:29875600-29875800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
40	chr22:29875600-29875800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr22:29875600-29875800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
42	chr22:29875600-29875800	Bivalent Enhancer	Primary T cells from cord blood	blood
43	chr22:29875600-29875800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
44	chr22:29875600-29875800	Flanking Active TSS	Fetal Brain Male	brain
45	chr22:29875600-29875800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
46	chr22:29875600-29875800	Bivalent/Poised TSS	HMEC	breast
47	chr22:29875600-29876000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
48	chr22:29875600-29876000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
49	chr22:29875600-29876200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr22:29875600-29876200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland

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