Variant report

Variant	rs17777927
Chromosome Location	chr4:56312633-56312634
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr4:56312217-56312944	SK-N-SH	brain:	n/a	n/a
2	SMC3	chr4:56312618-56312641	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr4:56312520-56312670	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr4:56312500-56312650	AoAF	blood vessel:	n/a	n/a
5	CTCF	chr4:56312540-56312690	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr4:56312589-56312653	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr4:56312540-56312690	AG09319	gingival:	n/a	n/a
8	CTCF	chr4:56312540-56312690	AG10803	skin:	n/a	n/a
9	CTCF	chr4:56312574-56312667	GM12878	blood:	n/a	n/a
10	CTCF	chr4:56312540-56312690	AG04449	skin:	n/a	n/a
11	TCF12	chr4:56311929-56312942	SK-N-SH	brain:	n/a	n/a
12	RAD21	chr4:56312494-56312698	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr4:56312560-56312710	HPF	lung:	n/a	n/a
14	CTCF	chr4:56312500-56312650	AG04449	skin:	n/a	n/a
15	CTCF	chr4:56312560-56312710	HPAF	blood vessel:	n/a	n/a
16	CTCF	chr4:56312540-56312690	NHDF-neo	bronchial:	n/a	n/a
17	CTCF	chr4:56312500-56312650	HCPEpiC	choroid plexus:	n/a	n/a
18	CTCF	chr4:56312540-56312690	AoAF	blood vessel:	n/a	n/a
19	CTCF	chr4:56312520-56312670	HMF	breast:	n/a	n/a
20	CTCF	chr4:56312560-56312710	Caco-2	colon:	n/a	n/a
21	CTCF	chr4:56312500-56312650	GM12874	blood:	n/a	n/a
22	CTCF	chr4:56312520-56312670	NHDF-neo	bronchial:	n/a	n/a
23	CTCF	chr4:56312560-56312710	HCPEpiC	choroid plexus:	n/a	n/a
24	CTCF	chr4:56312560-56312710	HMF	breast:	n/a	n/a
25	CTCF	chr4:56312540-56312690	HRPEpiC	eye:	n/a	n/a
26	CTCF	chr4:56312560-56312710	AG10803	skin:	n/a	n/a
27	CTCF	chr4:56312560-56312710	HRPEpiC	eye:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56309987..56312642-chr4:56314579..56316616,2	MCF-7	breast:

No data

Variant related genes	Relation type
CLOCK	TF binding region
ENSG00000134852	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1402963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1962453	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58476553	0.83[EUR][1000 genomes]
rs73817207	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 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	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:56274600-56332200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:56276000-56320000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:56279000-56321800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:56288400-56318400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:56290800-56340400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:56290800-56340600	Weak transcription	Thymus	Thymus
9	chr4:56293000-56324800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:56293000-56354800	Weak transcription	Aorta	Aorta
11	chr4:56294000-56341200	Weak transcription	Small Intestine	intestine
12	chr4:56296200-56314600	Weak transcription	Psoas Muscle	Psoas
13	chr4:56296200-56314600	Weak transcription	Hela-S3	cervix
14	chr4:56301600-56334800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:56301800-56313200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:56301800-56314000	Weak transcription	A549	lung
17	chr4:56301800-56314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:56301800-56316200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:56301800-56316200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:56301800-56318000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:56301800-56318000	Weak transcription	Right Ventricle	heart
22	chr4:56301800-56332200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:56301800-56339200	Weak transcription	Fetal Brain Male	brain
24	chr4:56302000-56314000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr4:56302200-56313200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:56302200-56313400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:56302200-56313600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:56302200-56314000	Weak transcription	Fetal Heart	heart
29	chr4:56302200-56314400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:56302200-56314800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:56302200-56315600	Weak transcription	Fetal Stomach	stomach
32	chr4:56302400-56375600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:56303000-56340200	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:56303600-56314200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:56304000-56331800	Weak transcription	Esophagus	oesophagus
36	chr4:56304600-56316200	Weak transcription	Lung	lung
37	chr4:56304600-56365600	Weak transcription	Spleen	Spleen
38	chr4:56304800-56314000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:56304800-56314600	Weak transcription	Colonic Mucosa	Colon
40	chr4:56304800-56331800	Weak transcription	Gastric	stomach
41	chr4:56304800-56340000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:56304800-56375800	Weak transcription	Pancreas	Pancrea
43	chr4:56305000-56314200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:56305000-56318200	Weak transcription	HSMMtube	muscle
45	chr4:56305200-56317800	Weak transcription	Brain Germinal Matrix	brain
46	chr4:56305600-56313600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:56305800-56314000	Weak transcription	Brain Anterior Caudate	brain
48	chr4:56306000-56313600	Weak transcription	Primary B cells from cord blood	blood
49	chr4:56306000-56314600	Weak transcription	HepG2	liver
50	chr4:56306000-56318200	Weak transcription	Brain Substantia Nigra	brain

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