Variant report

Variant	rs3794556
Chromosome Location	chr15:52851030-52851031
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr15:52850983-52851555	K562	blood:	n/a	n/a
2	POLR2A	chr15:52851008-52851107	H1-hESC	embryonic stem cell:	n/a	n/a
3	SETDB1	chr15:52850996-52851595	U2OS	brain:	n/a	n/a
4	POLR2A	chr15:52850960-52851765	GM12878	blood:	n/a	n/a
5	YY1	chr15:52850981-52851126	K562	blood:	n/a	n/a
6	POLR2A	chr15:52850984-52851235	K562	blood:	n/a	n/a
7	ZNF384	chr15:52850293-52851291	GM12878	blood:	n/a	n/a
8	NFIC	chr15:52850966-52852180	GM12878	blood:	n/a	n/a
9	KAP1	chr15:52850800-52851821	K562	blood:	n/a	n/a
10	POLR2A	chr15:52850953-52851286	GM12892	blood:	n/a	n/a
11	POLR2A	chr15:52850912-52852225	GM12892	blood:	n/a	n/a
12	ZNF384	chr15:52850517-52851348	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52844956..52846516-chr15:52850734..52853652,2	MCF-7	breast:
2	chr15:52819747..52821438-chr15:52850528..52853277,2	MCF-7	breast:

No data

Variant related genes	Relation type
ARPP19	TF binding region
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17651731	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17708230	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28790063	0.99[ASN][1000 genomes]
rs28861539	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 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	chr15:52836200-52851400	Weak transcription	Fetal Kidney	kidney
2	chr15:52836400-52855200	Weak transcription	Small Intestine	intestine
3	chr15:52837600-52852000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:52837800-52853000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:52838000-52853000	Strong transcription	Dnd41	blood
6	chr15:52838800-52859800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:52838800-52860000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:52839000-52851400	Weak transcription	Gastric	stomach
9	chr15:52839000-52851400	Weak transcription	Spleen	Spleen
10	chr15:52839000-52853400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:52839000-52858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:52839000-52859600	Weak transcription	Aorta	Aorta
13	chr15:52839200-52851800	Weak transcription	Right Ventricle	heart
14	chr15:52839200-52859200	Weak transcription	Colonic Mucosa	Colon
15	chr15:52841000-52857400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:52842400-52858400	Weak transcription	Pancreas	Pancrea
17	chr15:52842800-52851400	Weak transcription	Fetal Heart	heart
18	chr15:52843600-52852600	Weak transcription	Brain Substantia Nigra	brain
19	chr15:52844200-52852800	Weak transcription	Fetal Brain Female	brain
20	chr15:52844400-52855200	Weak transcription	Fetal Lung	lung
21	chr15:52844400-52859200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:52844600-52851200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:52844600-52851200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:52844600-52856400	Weak transcription	Ovary	ovary
25	chr15:52844600-52859000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:52844800-52851200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:52844800-52851800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:52844800-52860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:52845200-52851800	Weak transcription	Fetal Intestine Small	intestine
30	chr15:52845200-52854200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:52845200-52857200	Weak transcription	Fetal Stomach	stomach
32	chr15:52845800-52851800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:52845800-52853200	Strong transcription	Primary B cells from cord blood	blood
34	chr15:52846000-52851400	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:52846000-52851600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:52846200-52852200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:52846200-52852800	Weak transcription	Stomach Mucosa	stomach
38	chr15:52846200-52855800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:52846200-52857200	Weak transcription	Thymus	Thymus
40	chr15:52846200-52859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:52846200-52860000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr15:52847000-52859400	Weak transcription	Fetal Intestine Large	intestine
43	chr15:52847600-52852000	Strong transcription	HepG2	liver
44	chr15:52847800-52853000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:52848200-52852200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr15:52848200-52853200	Genic enhancers	K562	blood
47	chr15:52848600-52851800	Weak transcription	Brain Germinal Matrix	brain
48	chr15:52849000-52852800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr15:52849200-52851400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:52849200-52851400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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