Variant report

Variant	rs554009537
Chromosome Location	chr4:48342266-48342267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:48342228-48344387	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD1	chr4:48342148-48345930	IMR90	lung:	n/a	n/a
3	MYC	chr4:48342232-48344427	K562	blood:	n/a	n/a
4	EP300	chr4:48342258-48343664	K562	blood:	n/a	chr4:48343151-48343164 chr4:48343432-48343441 chr4:48343422-48343438 chr4:48343425-48343441
5	MTA3	chr4:48342241-48344676	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:48342143-48344570	PBDE	blood:	n/a	n/a
7	TBL1XR1	chr4:48342165-48343708	K562	blood:	n/a	n/a
8	CUX1	chr4:48342173-48343260	K562	blood:	n/a	n/a
9	MYC	chr4:48341842-48344580	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:48342263-48342313	BE2_C	brain:	n/a
2	chr4:48342263-48342313	GM06990	blood:	n/a
3	chr4:48342263-48342313	MCF10A-Er-Src	breast:	n/a
4	chr4:48342263-48342313	GM19239	blood:	n/a
5	chr4:48342263-48342313	AG10803	skin:	n/a
6	chr4:48342263-48342313	HCF	heart:	n/a
7	chr4:48342263-48342313	IMR90	lung:	fetal
8	chr4:48342263-48342313	HIPEpiC	eye:	n/a
9	chr4:48342263-48342313	ECC-1	luminal epithelium:	n/a
10	chr4:48342263-48342313	Caco-2	colon:	n/a
11	chr4:48342263-48342313	HCT-116	colon:	n/a
12	chr4:48342263-48342313	NH-A	brain:	n/a
13	chr4:48342263-48342313	HEK293	kidney:	embryo
14	chr4:48342263-48342313	HUVEC	blood vessel:	n/a
15	chr4:48342263-48342313	A549	lung:	n/a
16	chr4:48342263-48342313	SKMC	muscle:	n/a
17	chr4:48342263-48342313	NB4	blood:	n/a
18	chr4:48342263-48342313	HepG2	liver:	n/a
19	chr4:48342263-48342313	U87	brain:	n/a
20	chr4:48342263-48342313	HCPEpiC	choroid plexus:	n/a
21	chr4:48342263-48342313	AoSMC	blood vessel:	n/a
22	chr4:48342263-48342313	AG09319	gingival:	n/a
23	chr4:48342263-48342313	GM12891	blood:	n/a
24	chr4:48342263-48342313	ovcar-3	ovarian:	n/a
25	chr4:48342263-48342313	HRPEpiC	eye:	n/a
26	chr4:48342263-48342313	AG04450	lung:	fetal
27	chr4:48342263-48342313	AG09309	skin:	n/a
28	chr4:48342263-48342313	RPTEC	kidney:	n/a
29	chr4:48342263-48342313	ProgFib	skin:	n/a
30	chr4:48342263-48342313	Hela-S3	cervix:	n/a
31	chr4:48342263-48342313	GM12878	blood:	n/a
32	chr4:48342263-48342313	SK-N-SH	brain:	n/a
33	chr4:48342263-48342313	NHBE	bronchial:	n/a
34	chr4:48342263-48342313	SK-N-SH_RA	brain:	n/a
35	chr4:48342263-48342313	PrEC	prostate:	n/a
36	chr4:48342263-48342313	T-47D	breast:	n/a
37	chr4:48342263-48342313	H1-hESC	embryonic stem cell:	embryo
38	chr4:48342263-48342313	NT2-D1	testis:	n/a
39	chr4:48342263-48342313	GM12892	blood:	n/a
40	chr4:48342263-48342313	PFSK-1	brain:	n/a
41	chr4:48342263-48342313	HL-60	blood:	n/a
42	chr4:48342263-48342313	NHDF-neo	bronchial:	n/a
43	chr4:48342263-48342313	LNCaP	prostate:	n/a
44	chr4:48342263-48342313	SK-N-MC	brain:	n/a
45	chr4:48342263-48342313	Jurkat	blood:	n/a
46	chr4:48342263-48342313	HPAEpiC	pulmonary alveolar:	n/a
47	chr4:48342263-48342313	HRCEpiC	kidney:	n/a
48	chr4:48342263-48342313	K562	blood:	n/a
49	chr4:48342263-48342313	Hepatocyte	liver:	n/a
50	chr4:48342263-48342313	BJ	skin:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:48342222..48343122-chr6:10417159..10417982,2	Hela-S3	cervix:
2	chr4:48341542..48343650-chr4:48378558..48381453,2	K562	blood:
3	chr4:48339667..48343042-chr4:48377720..48381453,4	K562	blood:
4	chr4:48270141..48273598-chr4:48341900..48344865,7	K562	blood:
5	chr4:48341515..48344236-chr4:48506268..48509029,2	K562	blood:
6	chr4:48341290..48343185-chr4:52708590..52710145,2	K562	blood:
7	chr4:48309394..48311856-chr4:48341157..48342687,2	K562	blood:
8	chr4:48270358..48273390-chr4:48340605..48344777,4	MCF-7	breast:
9	chr4:48321470..48323955-chr4:48341055..48342680,2	K562	blood:
10	chr4:48341909..48343469-chr4:48483589..48486077,2	K562	blood:
11	chr4:48312456..48314197-chr4:48341222..48342911,2	K562	blood:

No data

Variant related genes	Relation type
SLAIN2	TF binding region
SLAIN2	CpG island
ENSG00000137203	Chromatin interaction
ENSG00000109184	Chromatin interaction
ENSG00000109171	Chromatin interaction
ENSG00000145248	Chromatin interaction
ENSG00000075539	Chromatin interaction
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv3377721	chr4:48342220-48345068	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
2	chr4:48333000-48342400	Weak transcription	Left Ventricle	heart
3	chr4:48334200-48342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:48334400-48342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:48337600-48342400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:48339400-48342400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:48340400-48342400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:48340800-48342400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:48341000-48342400	Weak transcription	Psoas Muscle	Psoas
10	chr4:48341200-48342400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:48341200-48342400	Weak transcription	Fetal Thymus	thymus
12	chr4:48341400-48342600	Flanking Active TSS	K562	blood
13	chr4:48341600-48342400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:48341600-48342600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:48341600-48342600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr4:48341800-48342400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:48341800-48342400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:48341800-48342600	Flanking Active TSS	NHLF	lung
19	chr4:48342000-48342400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:48342000-48342400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr4:48342000-48342400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr4:48342000-48342400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr4:48342000-48342400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr4:48342000-48342400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:48342000-48342600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:48342000-48342600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:48342000-48342600	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr4:48342000-48342600	Flanking Active TSS	Fetal Heart	heart
29	chr4:48342000-48342600	Flanking Active TSS	NHDF-Ad	bronchial
30	chr4:48342000-48342800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr4:48342000-48342800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:48342000-48343000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr4:48342000-48343000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr4:48342000-48345400	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr4:48342000-48345400	Active TSS	Fetal Intestine Large	intestine
36	chr4:48342000-48345600	Active TSS	Fetal Intestine Small	intestine
37	chr4:48342200-48342400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr4:48342200-48342400	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr4:48342200-48342400	Enhancers	Primary B cells from cord blood	blood
40	chr4:48342200-48342400	Enhancers	Primary B cells from peripheral blood	blood
41	chr4:48342200-48342400	Enhancers	Primary T cells from cord blood	blood
42	chr4:48342200-48342400	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr4:48342200-48342400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr4:48342200-48342400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr4:48342200-48342400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr4:48342200-48342400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:48342200-48342400	Enhancers	Brain Germinal Matrix	brain
48	chr4:48342200-48342400	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr4:48342200-48342400	Enhancers	Brain Substantia Nigra	brain
50	chr4:48342200-48342400	Enhancers	Colon Smooth Muscle	Colon

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