Variant report

Variant	rs3784139
Chromosome Location	chr14:69414322-69414323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr14:69414270-69415092	A549	lung:	n/a	chr14:69414834-69414852 chr14:69414618-69414634 chr14:69414618-69414634 chr14:69414613-69414639 chr14:69414618-69414634 chr14:69414613-69414639
2	POLR2A	chr14:69414198-69414354	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr14:69414165-69414399	A549	lung:	n/a	n/a
4	SP1	chr14:69414318-69414958	A549	lung:	n/a	chr14:69414412-69414419 chr14:69414364-69414378
5	NR3C1	chr14:69414178-69414965	A549	lung:	n/a	chr14:69414834-69414852 chr14:69414618-69414634 chr14:69414618-69414634 chr14:69414613-69414639 chr14:69414618-69414634 chr14:69414613-69414639

No.	Distal block	Cell Line	Cell type
1	chr14:69402982..69422523-chr14:69436263..69448017,46	MCF-7	breast:
2	chr14:69260918..69263431-chr14:69412114..69414632,2	MCF-7	breast:
3	chr14:69414297..69415812-chr14:69443551..69446042,2	K562	blood:
4	chr14:69402918..69410408-chr14:69410942..69415819,17	MCF-7	breast:
5	chr14:69403117..69416483-chr14:69441657..69449888,50	MCF-7	breast:

Variant related genes	Relation type
ACTN1	TF binding region
ENSG00000185650	Chromatin interaction
ENSG00000072110	Chromatin interaction
ENSG00000259062	Chromatin interaction
ENSG00000258531	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17106638	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17106640	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17757952	0.82[CEU][hapmap]
rs2268982	0.82[ASW][hapmap]
rs4902680	0.93[ASN][1000 genomes]
rs61981589	0.92[EUR][1000 genomes]

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	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv564964	chr14:69392264-69423164	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv456333	chr14:69392445-69415962	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv564965	chr14:69392445-69415962	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3784139	ZBTB25	cis	parietal	SCAN
rs3784139	SMOC1	cis	cerebellum	SCAN
rs3784139	SYNE2	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69387400-69420400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr14:69394200-69422200	Weak transcription	Dnd41	blood
3	chr14:69397800-69415200	Enhancers	Esophagus	oesophagus
4	chr14:69399000-69423200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr14:69400200-69416400	Enhancers	Pancreas	Pancrea
6	chr14:69400400-69417000	Enhancers	Fetal Muscle Leg	muscle
7	chr14:69400800-69420400	Enhancers	Fetal Lung	lung
8	chr14:69402000-69426200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr14:69402200-69425200	Enhancers	Right Atrium	heart
10	chr14:69402400-69414400	Enhancers	Adipose Nuclei	Adipose
11	chr14:69402400-69416400	Enhancers	Left Ventricle	heart
12	chr14:69402400-69423600	Enhancers	Fetal Heart	heart
13	chr14:69402400-69427000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:69402600-69416600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr14:69403600-69420400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr14:69404200-69417000	Enhancers	Right Ventricle	heart
17	chr14:69405000-69415400	Weak transcription	Psoas Muscle	Psoas
18	chr14:69406400-69417800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:69406800-69414400	Genic enhancers	Fetal Intestine Small	intestine
20	chr14:69407000-69414600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:69407000-69414600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr14:69407000-69419600	Weak transcription	Fetal Brain Male	brain
23	chr14:69407200-69414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:69407400-69416400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:69408400-69416400	Genic enhancers	Fetal Stomach	stomach
26	chr14:69408400-69416600	Enhancers	Brain Anterior Caudate	brain
27	chr14:69408400-69416600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr14:69408600-69414600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr14:69409400-69414800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
30	chr14:69409400-69416400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:69409600-69414400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr14:69409600-69414600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr14:69409800-69434400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr14:69410000-69414400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr14:69410000-69416200	Enhancers	Fetal Intestine Large	intestine
36	chr14:69410200-69416400	Enhancers	Lung	lung
37	chr14:69410200-69420200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr14:69410400-69416600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr14:69410600-69416600	Enhancers	Fetal Thymus	thymus
40	chr14:69410600-69418200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr14:69410800-69414800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:69410800-69416200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr14:69411000-69416400	Enhancers	Stomach Mucosa	stomach
44	chr14:69411200-69415400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr14:69411200-69416600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr14:69411200-69416800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr14:69411200-69442600	Weak transcription	Fetal Brain Female	brain
48	chr14:69411400-69416600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr14:69411400-69417800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr14:69411600-69414600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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