Variant report

Variant	rs17085734
Chromosome Location	chr4:56314286-56314287
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	NFIC	chr4:56313858-56314572	ECC-1	luminal epithelium:	n/a	n/a
2	PBX3	chr4:56313988-56314416	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr4:56313974-56314410	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr4:56313873-56314476	SK-N-SH	brain:	n/a	n/a
5	MAZ	chr4:56314280-56314329	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:56314013-56314427	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr4:56313802-56314561	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr4:56313876-56314424	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56312880..56314520-chr4:56319632..56321569,2	K562	blood:

Variant related genes	Relation type
CLOCK	TF binding region

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11725738	0.83[AFR][1000 genomes]
rs17085718	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17085837	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6810577	1.00[AMR][1000 genomes]
rs6820119	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6822752	0.87[AFR][1000 genomes]
rs6836071	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6848877	1.00[AMR][1000 genomes]
rs6854096	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7673760	1.00[AMR][1000 genomes]
rs7680567	1.00[AMR][1000 genomes]
rs7684685	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7686624	1.00[AMR][1000 genomes]
rs7692461	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][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:125 , 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	chr4:56301800-56316200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:56301800-56316200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:56301800-56318000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:56301800-56318000	Weak transcription	Right Ventricle	heart
19	chr4:56301800-56332200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:56301800-56339200	Weak transcription	Fetal Brain Male	brain
21	chr4:56302200-56314400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:56302200-56314800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:56302200-56315600	Weak transcription	Fetal Stomach	stomach
24	chr4:56302400-56375600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:56303000-56340200	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:56304000-56331800	Weak transcription	Esophagus	oesophagus
27	chr4:56304600-56316200	Weak transcription	Lung	lung
28	chr4:56304600-56365600	Weak transcription	Spleen	Spleen
29	chr4:56304800-56314600	Weak transcription	Colonic Mucosa	Colon
30	chr4:56304800-56331800	Weak transcription	Gastric	stomach
31	chr4:56304800-56340000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:56304800-56375800	Weak transcription	Pancreas	Pancrea
33	chr4:56305000-56318200	Weak transcription	HSMMtube	muscle
34	chr4:56305200-56317800	Weak transcription	Brain Germinal Matrix	brain
35	chr4:56306000-56314600	Weak transcription	HepG2	liver
36	chr4:56306000-56318200	Weak transcription	Brain Substantia Nigra	brain
37	chr4:56306000-56361200	Weak transcription	Stomach Mucosa	stomach
38	chr4:56306800-56314800	Strong transcription	Fetal Muscle Leg	muscle
39	chr4:56307400-56315400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:56307600-56340400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:56308800-56340400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr4:56309400-56314600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:56309400-56316200	Weak transcription	Fetal Lung	lung
44	chr4:56309400-56316200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:56310000-56314400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr4:56310000-56314600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:56310000-56314600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:56311200-56314400	Enhancers	Osteobl	bone
49	chr4:56311400-56317000	Strong transcription	Fetal Intestine Small	intestine
50	chr4:56311600-56315600	Weak transcription	Ovary	ovary

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