Variant report

Variant	rs1476498
Chromosome Location	chr17:45203877-45203878
allele	A/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	POLR2A	chr17:45203638-45204003	K562	blood:	n/a	n/a

Variant related genes	Relation type
CDC27	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1106950	0.95[CEU][hapmap]
rs11653589	0.85[JPT][hapmap]
rs1634265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1713493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851792	0.83[JPT][hapmap]
rs8068715	0.85[JPT][hapmap]
rs8071243	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs858670	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap]
rs858677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs858678	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs867859	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv908563	chr17:45158537-45230311	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv962456	chr17:45163689-45212872	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45185600-45206400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:45192400-45212800	Weak transcription	Gastric	stomach
3	chr17:45193200-45212800	Weak transcription	Aorta	Aorta
4	chr17:45194000-45209800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr17:45194200-45204600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:45194200-45208200	Strong transcription	HUVEC	blood vessel
7	chr17:45194200-45209600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:45194200-45209600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr17:45194200-45209800	Strong transcription	Dnd41	blood
10	chr17:45194800-45212800	Weak transcription	Colonic Mucosa	Colon
11	chr17:45194800-45214400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:45194800-45234200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:45195400-45209600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr17:45195400-45209800	Strong transcription	Fetal Thymus	thymus
15	chr17:45195600-45209400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:45195800-45212800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr17:45196000-45205600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr17:45196000-45206400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr17:45196000-45209600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:45196000-45209800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr17:45196200-45212800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:45196400-45204200	Weak transcription	Lung	lung
23	chr17:45196400-45204200	Weak transcription	Spleen	Spleen
24	chr17:45196400-45212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr17:45196400-45212800	Weak transcription	Ovary	ovary
26	chr17:45196600-45207400	Strong transcription	Placenta	Placenta
27	chr17:45196600-45213000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:45196600-45213000	Weak transcription	Esophagus	oesophagus
29	chr17:45197000-45207000	Strong transcription	Fetal Lung	lung
30	chr17:45197200-45206800	Strong transcription	GM12878-XiMat	blood
31	chr17:45197200-45207400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr17:45197200-45209600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr17:45197400-45206400	Strong transcription	Brain Germinal Matrix	brain
34	chr17:45197400-45206800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr17:45197400-45209800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr17:45197600-45207400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr17:45197600-45209600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:45197800-45209400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr17:45197800-45210000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr17:45198000-45206800	Strong transcription	Fetal Muscle Leg	muscle
41	chr17:45198000-45209600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:45198000-45212000	Strong transcription	Fetal Stomach	stomach
43	chr17:45198200-45205000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:45198200-45210200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:45198200-45212800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr17:45198200-45212800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr17:45198200-45212800	Weak transcription	Brain Angular Gyrus	brain
48	chr17:45198400-45204200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr17:45198400-45205000	Weak transcription	Brain Substantia Nigra	brain
50	chr17:45198400-45205800	Weak transcription	Rectal Smooth Muscle	rectum

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