Variant report

Variant	rs28410661
Chromosome Location	chr17:38331145-38331146
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	POLR2A	chr17:38330667-38331283	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr17:38330866-38331316	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr17:38331066-38331177	MCF-7	breast:	n/a	n/a
4	POLR2A	chr17:38330844-38331342	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38330070..38334400-chr17:38346938..38351108,4	K562	blood:
2	chr17:38177591..38179361-chr17:38330455..38332177,2	MCF-7	breast:

Variant related genes	Relation type
RAPGEFL1	TF binding region
ENSG00000008838	Chromatin interaction
ENSG00000108352	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs28750099	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7206995	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9896339	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9904120	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9906274	0.83[AFR][1000 genomes]
rs9909548	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9910546	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9911936	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 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	chr17:38297800-38333000	Strong transcription	Fetal Muscle Trunk	muscle
2	chr17:38297800-38336600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:38298200-38333000	Strong transcription	Fetal Thymus	thymus
4	chr17:38298600-38332200	Strong transcription	Fetal Intestine Small	intestine
5	chr17:38308200-38333200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr17:38314200-38333000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:38314800-38333200	Weak transcription	Right Atrium	heart
8	chr17:38315400-38331400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:38315600-38333000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:38315600-38333000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:38315800-38331400	Strong transcription	Fetal Intestine Large	intestine
12	chr17:38316200-38333200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr17:38316400-38331400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr17:38317000-38333000	Strong transcription	Spleen	Spleen
15	chr17:38317200-38333200	Strong transcription	Thymus	Thymus
16	chr17:38317400-38331200	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr17:38317400-38331400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr17:38317400-38333400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:38317400-38333800	Strong transcription	Dnd41	blood
20	chr17:38317600-38333000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr17:38317600-38333000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:38317600-38333200	Strong transcription	Left Ventricle	heart
23	chr17:38317800-38331400	Strong transcription	Lung	lung
24	chr17:38317800-38332800	Strong transcription	Brain Hippocampus Middle	brain
25	chr17:38318000-38331400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:38318000-38331400	Strong transcription	Brain Germinal Matrix	brain
27	chr17:38320600-38332800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:38322400-38332000	Strong transcription	Fetal Brain Female	brain
29	chr17:38322400-38333200	Weak transcription	Psoas Muscle	Psoas
30	chr17:38323800-38332800	Strong transcription	Right Ventricle	heart
31	chr17:38324600-38332400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:38324600-38332800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:38324600-38333000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:38324800-38331200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:38324800-38331200	Strong transcription	Fetal Lung	lung
36	chr17:38324800-38331400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr17:38324800-38331400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr17:38324800-38332000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:38324800-38332200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr17:38324800-38332200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:38324800-38332800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr17:38324800-38333000	Strong transcription	Fetal Stomach	stomach
43	chr17:38324800-38333200	Strong transcription	Adipose Nuclei	Adipose
44	chr17:38325000-38331400	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr17:38325000-38332400	Strong transcription	Fetal Muscle Leg	muscle
46	chr17:38325000-38333000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:38325000-38333000	Strong transcription	Placenta	Placenta
48	chr17:38325000-38333000	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr17:38325200-38331400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:38325200-38331600	Strong transcription	Brain Cingulate Gyrus	brain

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