Variant report

Variant	rs55662247
Chromosome Location	chr3:52718069-52718070
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:52717818-52721863	SK-N-SH	brain:	n/a	n/a
2	HCFC1	chr3:52717761-52720928	Hela-S3	cervix:	n/a	n/a
3	ZNF384	chr3:52717783-52718435	K562	blood:	n/a	n/a
4	CHD1	chr3:52717967-52718228	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52715353..52718281-chr3:52718433..52721429,4	MCF-7	breast:
2	chr3:52568115..52572187-chr3:52717267..52721555,8	K562	blood:
3	chr3:52707546..52709318-chr3:52716439..52718303,2	K562	blood:
4	chr3:52712073..52717938-chr3:52718038..52722104,14	K562	blood:
5	chr3:52701409..52703551-chr3:52716024..52719023,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252787	TF binding region
GNL3	TF binding region
PBRM1	TF binding region
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000163939	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17052329	0.84[AFR][1000 genomes]
rs17052401	1.00[AMR][1000 genomes]
rs59277755	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6803509	1.00[AMR][1000 genomes]
rs73839121	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839167	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839179	1.00[AMR][1000 genomes]
rs73839182	1.00[AMR][1000 genomes]
rs73839183	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:52665400-52719200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:52712600-52719400	Weak transcription	Gastric	stomach
5	chr3:52713200-52719200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:52713600-52718600	Enhancers	Adipose Nuclei	Adipose
7	chr3:52713600-52719200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:52713800-52718400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:52713800-52719200	Weak transcription	Aorta	Aorta
10	chr3:52714200-52718400	Weak transcription	Colonic Mucosa	Colon
11	chr3:52714200-52718400	Weak transcription	Stomach Mucosa	stomach
12	chr3:52714200-52718600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:52714200-52718800	Weak transcription	Right Atrium	heart
14	chr3:52714200-52718800	Weak transcription	Right Ventricle	heart
15	chr3:52714200-52719200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:52714200-52719200	Weak transcription	Esophagus	oesophagus
17	chr3:52714200-52719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:52714400-52718200	Weak transcription	HUVEC	blood vessel
19	chr3:52714400-52718600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:52714400-52718800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:52714600-52718200	Enhancers	NHLF	lung
22	chr3:52714600-52718600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:52714800-52718800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:52714800-52719000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr3:52715200-52718400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:52715200-52719000	Weak transcription	Placenta	Placenta
27	chr3:52715200-52719400	Weak transcription	Spleen	Spleen
28	chr3:52715400-52718600	Weak transcription	Psoas Muscle	Psoas
29	chr3:52715600-52718600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:52715800-52718200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:52715800-52718800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:52715800-52719000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr3:52716000-52718400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:52716000-52718800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:52716200-52719000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:52716200-52719200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:52716400-52718400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:52716400-52718600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:52716600-52718200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:52716600-52718400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:52716600-52718400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:52716600-52718400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:52716600-52718600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr3:52716600-52718600	Weak transcription	A549	lung
45	chr3:52716800-52718200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:52716800-52718200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:52716800-52718200	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:52716800-52718200	Weak transcription	HSMM	muscle
49	chr3:52716800-52718400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:52716800-52718400	Weak transcription	NHEK	skin

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