Variant report

Variant	rs73343250
Chromosome Location	chr20:25678042-25678043
allele	G/T
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	TAF1	chr20:25676660-25678080	ECC-1	luminal epithelium:	n/a	n/a
2	SREBP1	chr20:25676527-25679236	GM12878	blood:	n/a	n/a
3	SIX5	chr20:25677083-25678043	A549	lung:	n/a	chr20:25677955-25677964
4	POLR2A	chr20:25675981-25678253	MCF10A-Er-Src	breast:	n/a	n/a
5	GABPA	chr20:25676912-25678087	MCF-7	breast:	n/a	n/a
6	STAT3	chr20:25677507-25678371	MCF10A-Er-Src	breast:	n/a	chr20:25677704-25677715
7	REST	chr20:25676521-25678116	H1-neurons	neurons:	n/a	chr20:25677668-25677681 chr20:25676877-25676890
8	HCFC1	chr20:25676696-25678060	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr20:25675861-25678303	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25603699..25606216-chr20:25676779..25679090,3	MCF-7	breast:
2	chr15:91260044..91260612-chr20:25677141..25678100,2	Hela-S3	cervix:
3	chr20:25477099..25478848-chr20:25676437..25678716,2	MCF-7	breast:
4	chr20:25604068..25607059-chr20:25675582..25678596,4	MCF-7	breast:
5	chr20:25565180..25567156-chr20:25676091..25678288,2	MCF-7	breast:
6	chr20:25602422..25607796-chr20:25675112..25679388,9	K562	blood:
7	chr20:25602965..25606226-chr20:25676160..25678613,3	K562	blood:
8	chr15:51057473..51058014-chr20:25677690..25678458,2	Hela-S3	cervix:

Variant related genes	Relation type
ZNF337	TF binding region
ENSG00000197299	Chromatin interaction
ENSG00000101004	Chromatin interaction
ENSG00000259736	Chromatin interaction
ENSG00000170191	Chromatin interaction
ENSG00000138600	Chromatin interaction
ENSG00000213742	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs57150489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57870458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57982209	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59631229	1.00[EUR][1000 genomes]
rs6037213	1.00[EUR][1000 genomes]
rs6050738	1.00[EUR][1000 genomes]
rs61146844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6115245	1.00[EUR][1000 genomes]
rs61598299	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6515689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7267586	1.00[AMR][1000 genomes]
rs7273366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73334116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339340	1.00[AMR][1000 genomes]
rs73339342	1.00[AMR][1000 genomes]
rs73339354	1.00[AMR][1000 genomes]
rs73339363	1.00[AMR][1000 genomes]
rs73339381	1.00[AMR][1000 genomes]
rs73341321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341334	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73341366	1.00[AMR][1000 genomes]
rs73341383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343243	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343258	1.00[EUR][1000 genomes]
rs73343264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73343265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73345241	1.00[EUR][1000 genomes]
rs73345246	1.00[EUR][1000 genomes]
rs73345256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73348906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73348986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8118159	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8125097	1.00[EUR][1000 genomes]
rs8125218	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917415	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917456	1.00[AMR][1000 genomes]
rs9917460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9941767	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25675600-25678200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:25676000-25678400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:25676000-25678800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:25676200-25678200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr20:25676200-25678200	Active TSS	NHEK	skin
6	chr20:25676200-25678400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr20:25676200-25678400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr20:25676200-25678400	Active TSS	NHLF	lung
9	chr20:25676200-25678600	Active TSS	A549	lung
10	chr20:25676400-25678200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr20:25676400-25678200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr20:25676400-25678200	Active TSS	NHDF-Ad	bronchial
13	chr20:25676400-25678400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:25676400-25678400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:25676400-25678400	Active TSS	K562	blood
16	chr20:25676600-25678200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr20:25676600-25678200	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr20:25676600-25678200	Active TSS	HSMMtube	muscle
19	chr20:25676600-25678200	Active TSS	Osteobl	bone
20	chr20:25676600-25678400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr20:25676600-25678400	Active TSS	Fetal Brain Female	brain
22	chr20:25676600-25678600	Active TSS	HMEC	breast
23	chr20:25676600-25678800	Active TSS	Brain Germinal Matrix	brain
24	chr20:25676600-25679200	Active TSS	GM12878-XiMat	blood
25	chr20:25676800-25678200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr20:25676800-25678400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr20:25677000-25678400	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr20:25677400-25678200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr20:25677600-25678400	Active TSS	Right Atrium	heart
30	chr20:25677800-25678400	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr20:25677800-25678400	Active TSS	HepG2	liver
32	chr20:25677800-25678600	Weak transcription	Spleen	Spleen
33	chr20:25677800-25678800	Active TSS	Fetal Brain Male	brain
34	chr20:25677800-25701000	Weak transcription	Pancreas	Pancrea
35	chr20:25678000-25678400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr20:25678000-25678400	Enhancers	Primary B cells from cord blood	blood
37	chr20:25678000-25678400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr20:25678000-25678400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr20:25678000-25678400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr20:25678000-25678400	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr20:25678000-25678400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr20:25678000-25678400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr20:25678000-25678400	Enhancers	Adipose Nuclei	Adipose
44	chr20:25678000-25678400	Enhancers	Brain Anterior Caudate	brain
45	chr20:25678000-25678400	Enhancers	Fetal Lung	lung
46	chr20:25678000-25678400	Weak transcription	Right Ventricle	heart
47	chr20:25678000-25678400	Weak transcription	Thymus	Thymus
48	chr20:25678000-25678600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr20:25678000-25678600	Weak transcription	Brain Substantia Nigra	brain
50	chr20:25678000-25678600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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