Variant report

Variant	rs3888227
Chromosome Location	chr15:55790835-55790836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:134)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:134 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr15:55790412-55790877	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:55790258-55790926	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:55790301-55790877	U87	brain:	n/a	n/a
4	NR2C2	chr15:55790289-55790843	Hela-S3	cervix:	n/a	chr15:55790617-55790626
5	ELF1	chr15:55790267-55790935	GM12878	blood:	n/a	n/a
6	MAX	chr15:55790434-55790867	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:55790516-55790843	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr15:55790387-55790849	NB4	blood:	n/a	n/a
9	POLR2A	chr15:55790465-55790918	GM12892	blood:	n/a	n/a
10	SIN3AK20	chr15:55790011-55790886	MCF-7	breast:	n/a	n/a
11	SIN3A	chr15:55789978-55790835	H1-hESC	embryonic stem cell:	n/a	chr15:55790660-55790673
12	FOSL2	chr15:55790275-55790886	A549	lung:	n/a	n/a
13	POLR2A	chr15:55790376-55790941	PANC-1	pancreas:	n/a	n/a
14	MAX	chr15:55790279-55790889	K562	blood:	n/a	n/a
15	GABPA	chr15:55790151-55790898	A549	lung:	n/a	n/a
16	POLR2A	chr15:55790394-55790876	GM12892	blood:	n/a	n/a
17	POLR2A	chr15:55790286-55790887	Hela-S3	cervix:	n/a	n/a
18	MYC	chr15:55789714-55791063	A549	lung:	n/a	chr15:55790119-55790128 chr15:55790120-55790127
19	GABPA	chr15:55790023-55791064	MCF-7	breast:	n/a	n/a
20	HA-E2F1	chr15:55790292-55790868	MCF-7	breast:	n/a	chr15:55790660-55790670
21	MAX	chr15:55790253-55790846	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr15:55790071-55791023	A549	lung:	n/a	chr15:55790119-55790128 chr15:55790120-55790127
23	TAF1	chr15:55790459-55790887	PFSK-1	brain:	n/a	n/a
24	YY1	chr15:55790477-55790845	HCT-116	colon:	n/a	n/a
25	BCL3	chr15:55790292-55790938	A549	lung:	n/a	n/a
26	POLR2A	chr15:55790324-55791031	U87	brain:	n/a	n/a
27	POLR2A	chr15:55790206-55791038	SK-N-MC	brain:	n/a	n/a
28	MAX	chr15:55790204-55790876	Hela-S3	cervix:	n/a	n/a
29	MAX	chr15:55790164-55790869	SK-N-SH	brain:	n/a	n/a
30	GABPA	chr15:55790317-55790924	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr15:55790548-55790857	K562	blood:	n/a	n/a
32	GABPA	chr15:55790165-55790899	MCF-7	breast:	n/a	n/a
33	POLR2A	chr15:55790318-55791031	U87	brain:	n/a	n/a
34	GTF2F1	chr15:55790071-55790877	Hela-S3	cervix:	n/a	n/a
35	MAX	chr15:55790138-55790894	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr15:55790244-55791023	Hela-S3	cervix:	n/a	n/a
37	GABPA	chr15:55790274-55790919	HL-60	blood:	n/a	n/a
38	MXI1	chr15:55789653-55791517	SK-N-SH	brain:	n/a	chr15:55790581-55790596
39	POLR2A	chr15:55790261-55790860	H1-neurons	neurons:	n/a	n/a
40	MAX	chr15:55790123-55790914	A549	lung:	n/a	n/a
41	MAX	chr15:55790190-55790883	Hela-S3	cervix:	n/a	n/a
42	MAX	chr15:55790286-55790900	H1-hESC	embryonic stem cell:	n/a	n/a
43	SIN3AK20	chr15:55790070-55790888	MCF-7	breast:	n/a	n/a
44	MAX	chr15:55790325-55790843	H1-hESC	embryonic stem cell:	n/a	n/a
45	CHD2	chr15:55790264-55790852	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr15:55790286-55790904	HL-60	blood:	n/a	n/a
47	MXI1	chr15:55790039-55790853	H1-hESC	embryonic stem cell:	n/a	chr15:55790581-55790596
48	YY1	chr15:55790298-55790886	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr15:55790324-55790888	HUVEC	blood vessel:	n/a	n/a
50	MYC	chr15:55790449-55790869	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55609486..55611262-chr15:55788891..55791859,2	K562	blood:
2	chr15:55790459..55791055-chr21:48054984..48055756,2	HCT-116	colon:
3	chr1:222884982..222885886-chr15:55790504..55791243,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
DYX1C1-CCPG1	TF binding region
DYX1C1	TF binding region
ENSG00000225973	Chromatin interaction
ENSG00000186063	Chromatin interaction
ENSG00000160310	Chromatin interaction
ENSG00000069943	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12594443	0.90[ASN][1000 genomes]
rs16976349	0.90[ASN][1000 genomes]
rs7168397	0.92[ASN][1000 genomes]
rs7174998	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv833016	chr15:55749169-55897906	Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv817693	chr15:55788832-55809660	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55789600-55791400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:55789800-55791000	Active TSS	H1 Cell Line	embryonic stem cell
3	chr15:55789800-55791000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:55789800-55791000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:55789800-55791000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr15:55789800-55791000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:55789800-55791000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:55789800-55791000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr15:55789800-55791000	Active TSS	Fetal Lung	lung
10	chr15:55789800-55791200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:55789800-55791200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr15:55789800-55791200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:55789800-55791200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:55789800-55791200	Active TSS	Brain Germinal Matrix	brain
15	chr15:55789800-55791200	Active TSS	Colon Smooth Muscle	Colon
16	chr15:55789800-55791200	Active TSS	HMEC	breast
17	chr15:55789800-55791400	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr15:55789800-55791400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:55789800-55791800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr15:55790000-55791000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr15:55790000-55791000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr15:55790000-55791000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:55790000-55791000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr15:55790000-55791000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:55790000-55791000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:55790000-55791000	Active TSS	Brain Angular Gyrus	brain
27	chr15:55790000-55791000	Active TSS	Brain Hippocampus Middle	brain
28	chr15:55790000-55791000	Active TSS	Fetal Brain Male	brain
29	chr15:55790000-55791000	Active TSS	Fetal Muscle Trunk	muscle
30	chr15:55790000-55791000	Active TSS	Psoas Muscle	Psoas
31	chr15:55790000-55791000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr15:55790000-55791000	Active TSS	Right Ventricle	heart
33	chr15:55790000-55791000	Active TSS	HepG2	liver
34	chr15:55790000-55791000	Active TSS	NH-A	brain
35	chr15:55790000-55791000	Active TSS	NHLF	lung
36	chr15:55790000-55791200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr15:55790000-55791200	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr15:55790000-55791200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr15:55790000-55791200	Active TSS	Brain Anterior Caudate	brain
40	chr15:55790000-55791200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr15:55790000-55791200	Active TSS	Fetal Stomach	stomach
42	chr15:55790000-55791200	Active TSS	Right Atrium	heart
43	chr15:55790000-55791200	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr15:55790000-55791200	Active TSS	A549	lung
45	chr15:55790000-55791200	Active TSS	GM12878-XiMat	blood
46	chr15:55790000-55791400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr15:55790000-55791400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:55790000-55791400	Active TSS	Fetal Kidney	kidney
49	chr15:55790000-55791400	Active TSS	Rectal Smooth Muscle	rectum
50	chr15:55790000-55791400	Active TSS	K562	blood

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