Variant report

Variant	rs4520895
Chromosome Location	chr17:45169760-45169761
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45169541..45171629-chr17:45172586..45174850,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12450537	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630431	1.00[ASN][1000 genomes]
rs1634272	0.86[ASN][1000 genomes]
rs2004580	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316667	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4061304	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4387650	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968305	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58675395	0.86[ASN][1000 genomes]
rs62074463	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8064557	1.00[ASN][1000 genomes]
rs8073829	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894300	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897338	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911627	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	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
6	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
7	esv21010	chr17:45125753-45177221	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	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
10	nsv521632	chr17:45151549-45196190	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	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
12	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4520895	RP11-156P1.3	cis	lung	GTEx
rs4520895	RP11-156P1.3	cis	Thyroid	GTEx
rs4520895	RP11-156P1.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45145000-45169800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:45145000-45169800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:45145000-45169800	Weak transcription	Fetal Lung	lung
4	chr17:45145000-45176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr17:45145000-45176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:45145000-45176800	Weak transcription	Lung	lung
7	chr17:45145200-45170200	Weak transcription	Brain Germinal Matrix	brain
8	chr17:45145200-45176600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr17:45145400-45176000	Weak transcription	Primary T cells from cord blood	blood
10	chr17:45146400-45169800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr17:45146400-45170800	Weak transcription	Dnd41	blood
12	chr17:45148800-45175400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr17:45149000-45170000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:45149000-45173800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr17:45149600-45175400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr17:45149600-45176800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr17:45150200-45170000	Weak transcription	Ovary	ovary
18	chr17:45150200-45174600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:45150600-45169800	Weak transcription	Fetal Muscle Leg	muscle
20	chr17:45150600-45170600	Weak transcription	HSMM	muscle
21	chr17:45150600-45176400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr17:45150600-45176800	Weak transcription	Left Ventricle	heart
23	chr17:45155000-45169800	Weak transcription	Fetal Brain Female	brain
24	chr17:45155600-45170200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:45155600-45170200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:45155600-45170200	Weak transcription	NHEK	skin
27	chr17:45155600-45173600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:45158200-45170600	Weak transcription	A549	lung
29	chr17:45158600-45169800	Weak transcription	Fetal Thymus	thymus
30	chr17:45158600-45175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:45159200-45175600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr17:45159600-45169800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr17:45159800-45169800	Weak transcription	Fetal Stomach	stomach
34	chr17:45159800-45170200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:45162600-45170000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr17:45163200-45170200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr17:45163200-45176800	Weak transcription	Fetal Intestine Large	intestine
38	chr17:45163400-45170200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr17:45163800-45175000	Weak transcription	HepG2	liver
40	chr17:45164200-45169800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:45164200-45170600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr17:45164600-45174000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr17:45164800-45176600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr17:45165400-45170200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr17:45165800-45170400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr17:45166200-45176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:45167200-45169800	Weak transcription	Fetal Intestine Small	intestine
48	chr17:45167600-45177000	Weak transcription	Spleen	Spleen
49	chr17:45168400-45170200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:45168400-45176000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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