Variant report

Variant	rs542005789
Chromosome Location	chr3:49967821-49967822
allele	A/C
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:9)
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	HCFC1	chr3:49966646-49967880	Hela-S3	cervix:	n/a	n/a
2	MAX	chr3:49966622-49967834	HepG2	liver:	n/a	n/a
3	JUN	chr3:49966690-49967837	K562	blood:	n/a	chr3:49966767-49966776
4	POLR2A	chr3:49966780-49968209	HepG2	liver:	n/a	n/a
5	E2F4	chr3:49967122-49967933	MCF10A-Er-Src	breast:	n/a	n/a
6	MAZ	chr3:49966618-49967948	IMR90	lung:	n/a	n/a
7	REST	chr3:49966500-49967823	H1-neurons	neurons:	n/a	chr3:49967406-49967419 chr3:49967409-49967422 chr3:49967391-49967409
8	MXI1	chr3:49966578-49969002	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr3:49966799-49967874	K562	blood:	n/a	n/a
10	POLR2A	chr3:49966824-49967868	HUVEC	blood vessel:	n/a	n/a
11	MAX	chr3:49966607-49967910	HCT-116	colon:	n/a	n/a
12	ZNF384	chr3:49967155-49967980	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49892535..49894935-chr3:49965699..49968471,2	K562	blood:
2	chr3:49965505..49970003-chr3:49975811..49980300,11	K562	blood:
3	chr3:49840341..49842910-chr3:49967049..49969753,2	K562	blood:
4	chr3:49965568..49971141-chr3:49975411..49979217,7	MCF-7	breast:
5	chr3:49966957..49970009-chr3:49975972..49978983,5	MCF-7	breast:
6	chr3:49965505..49970003-chr3:49974970..49980028,17	K562	blood:
7	chr3:49966031..49968659-chr3:50125180..50127794,3	K562	blood:
8	chr3:49750537..49752087-chr3:49966182..49968764,2	K562	blood:
9	chr3:49966762..49969614-chr3:50125142..50129125,3	K562	blood:

No data

Variant related genes	Relation type
MON1A	TF binding region
ENSG00000003756	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000183763	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv965334	chr3:49967342-50000012	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49966000-49968200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr3:49966200-49968000	Active TSS	Psoas Muscle	Psoas
3	chr3:49966200-49968200	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:49966400-49968000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:49966400-49968000	Active TSS	Brain Cingulate Gyrus	brain
6	chr3:49966400-49968000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr3:49966400-49968000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:49966400-49968000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:49966600-49968000	Active TSS	Right Atrium	heart
10	chr3:49966600-49968000	Active TSS	K562	blood
11	chr3:49966600-49968200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:49966600-49968200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:49966800-49968000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr3:49967000-49968000	Active TSS	Colonic Mucosa	Colon
15	chr3:49967200-49968000	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr3:49967200-49968200	Active TSS	HepG2	liver
17	chr3:49967400-49968000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:49967400-49968000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr3:49967400-49968000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:49967400-49968000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:49967400-49968000	Flanking Active TSS	Fetal Intestine Large	intestine
22	chr3:49967400-49968000	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr3:49967400-49968200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:49967400-49968200	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr3:49967400-49968200	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr3:49967600-49968000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:49967600-49968000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:49967600-49968000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:49967600-49968000	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr3:49967600-49968000	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:49967600-49968200	Active TSS	Primary hematopoietic stem cells	blood
32	chr3:49967600-49968200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:49967600-49968200	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr3:49967600-49968200	Enhancers	Esophagus	oesophagus
35	chr3:49967600-49968200	Enhancers	Fetal Heart	heart
36	chr3:49967600-49968200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr3:49967600-49968400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:49967600-49968400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:49967600-49968400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr3:49967600-49968400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:49967600-49968400	Weak transcription	Spleen	Spleen
42	chr3:49967600-49968800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:49967600-49969000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:49967600-49969200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:49967600-49969200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr3:49967600-49977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:49967800-49968000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:49967800-49968000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:49967800-49968000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr3:49967800-49968000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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