Variant report

Variant	rs549001
Chromosome Location	chr3:119395211-119395212
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119394854-119396781	U87	brain:	n/a	n/a
2	POLR2A	chr3:119395196-119396925	U87	brain:	n/a	n/a
3	POLR2A	chr3:119394473-119396840	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:119394816-119396770	GM19099	blood:	n/a	n/a
5	POLR2A	chr3:119394983-119395805	GM12878	blood:	n/a	n/a
6	CUX1	chr3:119395114-119395223	GM12878	blood:	n/a	n/a
7	GATA1	chr3:119394665-119396732	PBDE	blood:	n/a	chr3:119395225-119395236
8	POLR2A	chr3:119394618-119396838	GM12892	blood:	n/a	n/a
9	GATA3	chr3:119394082-119395232	SH-SY5Y	brain:	n/a	n/a
10	POLR2A	chr3:119395196-119396986	U87	brain:	n/a	n/a
11	POLR2A	chr3:119394507-119396828	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:119394772-119396781	U87	brain:	n/a	n/a
13	POLR2A	chr3:119394788-119396746	GM18505	blood:	n/a	n/a
14	POLR2A	chr3:119394681-119396716	K562	blood:	n/a	n/a
15	NFATC1	chr3:119395127-119395832	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:119394547-119395250	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:119394872-119395819	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:119394629-119396828	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:119395090-119396954	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr3:119394927-119395213	GM12891	blood:	n/a	n/a
21	HCFC1	chr3:119395206-119396830	Hela-S3	cervix:	n/a	n/a
22	MTA3	chr3:119394548-119396962	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:119394620-119396857	GM12891	blood:	n/a	n/a
24	POLR2A	chr3:119394608-119395827	GM12892	blood:	n/a	n/a
25	POLR2A	chr3:119394435-119396804	GM12892	blood:	n/a	n/a
26	POLR2A	chr3:119394835-119395853	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr3:119394577-119395808	GM12891	blood:	n/a	n/a
28	POLR2A	chr3:119395196-119396743	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119217361..119219124-chr3:119394788..119396855,3	MCF-7	breast:
2	chr3:119371437..119373754-chr3:119392688..119396112,3	K562	blood:
3	chr3:119383202..119386543-chr3:119393770..119396267,3	MCF-7	breast:
4	chr3:119215976..119218932-chr3:119393949..119396539,3	K562	blood:
5	chr3:119181523..119183291-chr3:119394912..119396579,2	MCF-7	breast:
6	chr3:119215767..119217677-chr3:119394561..119396315,2	MCF-7	breast:
7	chr3:119297880..119300098-chr3:119394986..119397161,3	MCF-7	breast:
8	chr3:119393569..119396281-chr3:119421855..119424087,2	MCF-7	breast:
9	chr3:119040381..119043387-chr3:119393976..119396207,3	K562	blood:
10	chr3:119394727..119396286-chr3:119814089..119815777,2	K562	blood:

No data

Variant related genes	Relation type
COX17	TF binding region
ENSG00000242622	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000272662	Chromatin interaction
ENSG00000121577	Chromatin interaction
ENSG00000144843	Chromatin interaction
ENSG00000272967	Chromatin interaction
ENSG00000183833	Chromatin interaction
ENSG00000241155	Chromatin interaction
ENSG00000176142	Chromatin interaction

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

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

rs_ID	r²[population]
rs1720143	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1806759	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2688636	0.89[AFR][1000 genomes]
rs491166	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr3:119392200-119395400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119393000-119395400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:119393600-119395400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:119393600-119395600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:119393600-119395600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:119393600-119395600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:119393600-119395600	Weak transcription	Esophagus	oesophagus
8	chr3:119393600-119395600	Weak transcription	Gastric	stomach
9	chr3:119393600-119395600	Weak transcription	Lung	lung
10	chr3:119393600-119395600	Weak transcription	Pancreas	Pancrea
11	chr3:119393600-119395600	Weak transcription	Spleen	Spleen
12	chr3:119393800-119395400	Weak transcription	Ovary	ovary
13	chr3:119394200-119395400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:119394400-119395400	Enhancers	Stomach Mucosa	stomach
15	chr3:119394600-119395400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:119394600-119395400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:119394600-119395400	Enhancers	Primary B cells from cord blood	blood
18	chr3:119394600-119395400	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:119394600-119395400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:119394600-119395400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr3:119394600-119395400	Flanking Active TSS	A549	lung
22	chr3:119394600-119395400	Flanking Active TSS	Hela-S3	cervix
23	chr3:119394600-119395600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:119394600-119395600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr3:119394600-119395600	Enhancers	Small Intestine	intestine
26	chr3:119394600-119395600	Flanking Active TSS	Dnd41	blood
27	chr3:119394600-119395800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr3:119394600-119396600	Active TSS	Left Ventricle	heart
29	chr3:119394800-119395400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:119394800-119395400	Flanking Active TSS	Fetal Brain Male	brain
31	chr3:119394800-119395400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr3:119394800-119395400	Flanking Active TSS	HepG2	liver
33	chr3:119394800-119395400	Flanking Active TSS	K562	blood
34	chr3:119394800-119395600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:119394800-119395600	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr3:119394800-119395600	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr3:119394800-119395800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr3:119394800-119395800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr3:119394800-119395800	Flanking Active TSS	Liver	Liver
40	chr3:119394800-119395800	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr3:119394800-119395800	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr3:119394800-119395800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr3:119394800-119396600	Active TSS	GM12878-XiMat	blood
44	chr3:119394800-119396800	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:119394800-119396800	Active TSS	Colonic Mucosa	Colon
46	chr3:119394800-119396800	Active TSS	Psoas Muscle	Psoas
47	chr3:119394800-119396800	Active TSS	Right Ventricle	heart
48	chr3:119395000-119395400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:119395000-119395400	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr3:119395000-119395400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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