Variant report

Variant	rs56993164
Chromosome Location	chr3:139107233-139107234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr3:139106950-139107331	K562	blood:	n/a	chr3:139107157-139107168
2	POLR2A	chr3:139106121-139107410	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:139106214-139110153	IMR90	lung:	n/a	n/a
4	POLR2A	chr3:139106152-139107321	MCF10A-Er-Src	breast:	n/a	n/a
5	ZNF384	chr3:139107012-139107342	K562	blood:	n/a	n/a
6	TBL1XR1	chr3:139107057-139107248	K562	blood:	n/a	n/a
7	POLR2A	chr3:139106309-139107394	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:139066912..139069879-chr3:139106229..139109511,3	K562	blood:
2	chr3:139062965..139064621-chr3:139106496..139109082,2	MCF-7	breast:
3	chr3:139062813..139064566-chr3:139107029..139109039,2	MCF-7	breast:
4	chr3:139061660..139066893-chr3:139105523..139110764,11	K562	blood:
5	chr3:139088868..139091914-chr3:139107086..139109851,3	K562	blood:
6	chr3:139063205..139066777-chr3:139105523..139110764,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000248932	TF binding region
ENSG00000184432	Chromatin interaction
ENSG00000175110	Chromatin interaction
ENSG00000272656	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10513063	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1602626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602628	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17316181	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17335312	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17394620	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17395611	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17494356	0.85[ASN][1000 genomes]
rs17560106	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1844977	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289348	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2289350	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2291555	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2307031	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772876	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs41356949	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs41399544	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55922868	0.90[ASN][1000 genomes]
rs57356584	0.89[EUR][1000 genomes]
rs57995350	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58060926	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59628512	0.90[ASN][1000 genomes]
rs59958973	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59960641	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61034702	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61613889	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61680644	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139084800-139107800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:139092200-139107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:139092400-139107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:139095000-139107600	Weak transcription	Lung	lung
5	chr3:139095200-139108000	Weak transcription	Spleen	Spleen
6	chr3:139098200-139107600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:139099200-139107800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:139101600-139107600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:139102200-139107600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:139103600-139107800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:139104600-139107600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:139104600-139107600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:139104800-139107400	Enhancers	Adipose Nuclei	Adipose
14	chr3:139105600-139107400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:139106000-139107400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:139106000-139107400	Enhancers	Stomach Mucosa	stomach
17	chr3:139106000-139107600	Enhancers	Fetal Brain Male	brain
18	chr3:139106200-139107400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:139106200-139107400	Enhancers	Brain Angular Gyrus	brain
20	chr3:139106200-139107400	Enhancers	Brain Anterior Caudate	brain
21	chr3:139106200-139107400	Enhancers	Brain Hippocampus Middle	brain
22	chr3:139106200-139107400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:139106200-139107400	Enhancers	Brain Substantia Nigra	brain
24	chr3:139106200-139107400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr3:139106200-139107400	Flanking Active TSS	Dnd41	blood
26	chr3:139106200-139107600	Enhancers	Primary hematopoietic stem cells	blood
27	chr3:139106200-139107600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr3:139106200-139107600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:139106200-139107600	Enhancers	Brain Cingulate Gyrus	brain
30	chr3:139106400-139107600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr3:139106400-139107800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr3:139106400-139109400	Active TSS	Stomach Smooth Muscle	stomach
33	chr3:139106400-139109600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:139106400-139109800	Active TSS	HSMMtube	muscle
35	chr3:139106600-139107400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:139106600-139107400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:139106600-139107600	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:139106600-139108000	Active TSS	Brain Germinal Matrix	brain
39	chr3:139106600-139109600	Active TSS	NHLF	lung
40	chr3:139106600-139110400	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr3:139106800-139107400	Enhancers	Primary B cells from cord blood	blood
42	chr3:139106800-139107400	Weak transcription	Fetal Brain Female	brain
43	chr3:139106800-139107400	Flanking Active TSS	HUVEC	blood vessel
44	chr3:139106800-139107600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:139106800-139107800	Active TSS	HepG2	liver
46	chr3:139106800-139109400	Active TSS	Aorta	Aorta
47	chr3:139106800-139109600	Active TSS	Right Ventricle	heart
48	chr3:139106800-139109600	Active TSS	NHDF-Ad	bronchial
49	chr3:139106800-139109800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:139106800-139109800	Active TSS	iPS-20b Cell Line	embryonic stem cell

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