Variant report

Variant	rs28579392
Chromosome Location	chr4:119662538-119662539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:119662500-119662650	NHLF	lung:	n/a	n/a
2	POLR2A	chr4:119661838-119662917	K562	blood:	n/a	n/a
3	RAD21	chr4:119661622-119663159	SK-N-SH	brain:	n/a	chr4:119662222-119662234 chr4:119662217-119662236
4	CTCF	chr4:119662460-119662690	HPAF	blood vessel:	n/a	n/a
5	SMC3	chr4:119662039-119662605	Hela-S3	cervix:	n/a	chr4:119662218-119662232
6	RAD21	chr4:119662015-119662707	SK-N-SH_RA	brain:	n/a	chr4:119662222-119662234 chr4:119662217-119662236
7	CTCF	chr4:119662021-119662626	K562	blood:	n/a	chr4:119662218-119662239 chr4:119662216-119662234 chr4:119662221-119662231 chr4:119662219-119662232 chr4:119662217-119662233
8	CTCF	chr4:119662420-119662570	GM12873	blood:	n/a	n/a
9	CTCF	chr4:119662440-119662590	BE2_C	brain:	n/a	n/a
10	RAD21	chr4:119661993-119662884	SK-N-SH_RA	brain:	n/a	chr4:119662222-119662234 chr4:119662217-119662236
11	CTCF	chr4:119662420-119662570	AG09319	gingival:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:119662530-119662580	K562	blood:	n/a
2	chr4:119662530-119662580	HUVEC	blood vessel:	n/a
3	chr4:119662530-119662580	HEK293	kidney:	embryo
4	chr4:119662530-119662580	HPAEpiC	pulmonary alveolar:	n/a
5	chr4:119662530-119662580	CMK	blood:	n/a
6	chr4:119662530-119662580	MCF10A-Er-Src	breast:	n/a
7	chr4:119662530-119662580	SAEC	small airway:	n/a
8	chr4:119662530-119662580	T-47D	breast:	n/a
9	chr4:119662530-119662580	AG04449	skin:	fetal
10	chr4:119662530-119662580	H1-hESC	embryonic stem cell:	embryo
11	chr4:119662530-119662580	LNCaP	prostate:	n/a
12	chr4:119662530-119662580	AG04450	lung:	fetal
13	chr4:119662530-119662580	GM12891	blood:	n/a
14	chr4:119662530-119662580	MCF-7	breast:	n/a
15	chr4:119662530-119662580	NB4	blood:	n/a
16	chr4:119662530-119662580	HRPEpiC	eye:	n/a
17	chr4:119662530-119662580	HCM	heart:	n/a
18	chr4:119662530-119662580	HCPEpiC	choroid plexus:	n/a
19	chr4:119662530-119662580	NHDF-neo	bronchial:	n/a
20	chr4:119662530-119662580	AG10803	skin:	n/a
21	chr4:119662530-119662580	HCF	heart:	n/a
22	chr4:119662530-119662580	SKMC	muscle:	n/a
23	chr4:119662530-119662580	Hepatocyte	liver:	n/a
24	chr4:119662530-119662580	A549	lung:	n/a
25	chr4:119662530-119662580	ProgFib	skin:	n/a
26	chr4:119662530-119662580	NT2-D1	testis:	n/a
27	chr4:119662530-119662580	BE2_C	brain:	n/a
28	chr4:119662530-119662580	HMEC	breast:	n/a
29	chr4:119662530-119662580	ECC-1	luminal epithelium:	n/a
30	chr4:119662530-119662580	SK-N-SH_RA	brain:	n/a
31	chr4:119662530-119662580	NHBE	bronchial:	n/a
32	chr4:119662530-119662580	U87	brain:	n/a
33	chr4:119662530-119662580	HRCEpiC	kidney:	n/a
34	chr4:119662530-119662580	GM19239	blood:	n/a
35	chr4:119662530-119662580	Hela-S3	cervix:	n/a
36	chr4:119662530-119662580	HEEpiC	esophagus:	n/a
37	chr4:119662530-119662580	Caco-2	colon:	n/a
38	chr4:119662530-119662580	BJ	skin:	n/a
39	chr4:119662530-119662580	SK-N-SH	brain:	n/a
40	chr4:119662530-119662580	AoSMC	blood vessel:	n/a
41	chr4:119662530-119662580	HRE	kidney:	n/a
42	chr4:119662530-119662580	HepG2	liver:	n/a
43	chr4:119662530-119662580	Jurkat	blood:	n/a
44	chr4:119662530-119662580	HAEpiC	amniotic membrane:	n/a
45	chr4:119662530-119662580	PANC-1	pancreas:	n/a
46	chr4:119662530-119662580	HL-60	blood:	n/a
47	chr4:119662530-119662580	GM06990	blood:	n/a
48	chr4:119662530-119662580	PFSK-1	brain:	n/a
49	chr4:119662530-119662580	RPTEC	kidney:	n/a
50	chr4:119662530-119662580	GM12892	blood:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:119661926..119662579-chr4:119890197..119891151,3	MCF-7	breast:
2	chr4:119661779..119662689-chr4:119786436..119786955,2	K562	blood:
3	chr4:119662372..119664026-chr4:119756152..119757934,2	MCF-7	breast:
4	chr4:119661708..119662728-chr4:119811010..119811893,7	MCF-7	breast:
5	chr4:119662280..119663846-chr4:120132859..120135292,2	MCF-7	breast:
6	chr4:119661756..119662694-chr4:119811343..119812031,3	K562	blood:

No data

Variant related genes	Relation type
SEC24D	TF binding region
SEC24D	CpG island
ENSG00000178636	Chromatin interaction
ENSG00000150961	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10011981	0.86[AFR][1000 genomes]
rs10016306	0.81[AFR][1000 genomes]
rs10018497	0.86[AFR][1000 genomes]
rs10029461	0.86[AFR][1000 genomes]
rs10471011	0.86[AFR][1000 genomes]
rs28451017	0.86[AFR][1000 genomes]
rs28473188	0.81[AFR][1000 genomes]
rs28488961	0.87[AFR][1000 genomes]
rs28551135	0.86[AFR][1000 genomes]
rs28572113	0.86[AFR][1000 genomes]
rs28609351	0.86[AFR][1000 genomes]
rs28736670	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28854838	0.87[AFR][1000 genomes]
rs28878302	0.86[AFR][1000 genomes]
rs9985565	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
3	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
4	chr4:119630400-119674200	Weak transcription	A549	lung
5	chr4:119633200-119662800	Weak transcription	Brain Anterior Caudate	brain
6	chr4:119633400-119667600	Weak transcription	Brain Germinal Matrix	brain
7	chr4:119640800-119692600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr4:119641600-119679800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr4:119642000-119666800	Strong transcription	Placenta	Placenta
10	chr4:119642200-119668200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr4:119642400-119668400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:119644400-119667400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:119645400-119668200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:119646200-119667000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:119649200-119665200	Weak transcription	Small Intestine	intestine
16	chr4:119649200-119666800	Weak transcription	Psoas Muscle	Psoas
17	chr4:119649200-119670600	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:119649200-119675200	Weak transcription	Brain Substantia Nigra	brain
19	chr4:119649200-119687600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:119649200-119693600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:119649600-119664600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:119650600-119668400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:119651400-119664600	Weak transcription	Fetal Brain Male	brain
24	chr4:119651800-119665400	Strong transcription	HUVEC	blood vessel
25	chr4:119651800-119672600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:119651800-119687400	Weak transcription	Thymus	Thymus
27	chr4:119652000-119672400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:119653200-119663800	Weak transcription	Esophagus	oesophagus
29	chr4:119653400-119668400	Strong transcription	HepG2	liver
30	chr4:119654400-119662600	Weak transcription	Gastric	stomach
31	chr4:119654400-119666200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:119654400-119672600	Strong transcription	NH-A	brain
33	chr4:119654400-119687400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:119654800-119676000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:119655200-119662600	Strong transcription	Osteobl	bone
36	chr4:119655400-119672800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr4:119655600-119665400	Strong transcription	Fetal Muscle Leg	muscle
38	chr4:119656200-119667800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:119656400-119662800	Strong transcription	Colonic Mucosa	Colon
40	chr4:119657200-119662600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr4:119657400-119663000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr4:119657600-119663800	Weak transcription	Fetal Intestine Small	intestine
43	chr4:119659000-119667200	Strong transcription	HSMMtube	muscle
44	chr4:119659200-119668000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:119659600-119663800	Weak transcription	Spleen	Spleen
46	chr4:119659600-119666600	Weak transcription	Right Ventricle	heart
47	chr4:119659600-119690400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:119660000-119672800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:119660200-119663200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:119660200-119668000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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