Variant report

Variant	rs3809869
Chromosome Location	chr17:45904163-45904164
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	chr17:45904120-45904176	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45902742..45905383-chr17:45921555..45923450,2	MCF-7	breast:

Variant related genes	Relation type
OSBPL7	TF binding region
LRRC46	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1005655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11079795	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11079796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11650289	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11650536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11652439	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11869958	0.95[CHB][hapmap]
rs11870002	0.95[CHB][hapmap]
rs16948401	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16948590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16948722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1985407	0.89[CHB][hapmap]
rs2001381	0.81[MEX][hapmap];0.86[TSI][hapmap]
rs2074188	0.95[CHB][hapmap]
rs2074189	0.95[CHB][hapmap]
rs701984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72833426	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878171	0.86[CHB][hapmap]
rs9674817	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3809869	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs3809869	RPL27	cis	cerebellum	SCAN
rs3809869	VAT1	cis	cerebellum	SCAN
rs3809869	SCRN2	cis	Whole Blood	GTEx
rs3809869	OSBPL7	cis	Thyroid	GTEx
rs3809869	CALCOCO2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45899800-45904400	Weak transcription	Small Intestine	intestine
2	chr17:45899800-45908000	Weak transcription	Right Atrium	heart
3	chr17:45900200-45906400	Strong transcription	Fetal Intestine Small	intestine
4	chr17:45900200-45906800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:45900200-45907000	Strong transcription	Primary T cells from cord blood	blood
6	chr17:45900400-45904400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:45900400-45905800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:45900400-45906200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:45900400-45906200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:45900400-45906200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:45900400-45906200	Strong transcription	Brain Hippocampus Middle	brain
12	chr17:45900400-45906400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:45900400-45906400	Strong transcription	Liver	Liver
14	chr17:45900400-45906400	Strong transcription	Brain Germinal Matrix	brain
15	chr17:45900400-45906400	Strong transcription	Fetal Intestine Large	intestine
16	chr17:45900400-45906400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr17:45900400-45907200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr17:45900400-45907400	Weak transcription	Fetal Heart	heart
19	chr17:45900400-45907400	Strong transcription	Fetal Stomach	stomach
20	chr17:45900600-45905600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:45900600-45906200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:45900600-45906200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr17:45900600-45906200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:45900600-45906200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr17:45900600-45906200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr17:45900600-45906200	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr17:45900600-45906200	Strong transcription	Brain Anterior Caudate	brain
28	chr17:45900600-45906200	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr17:45900600-45906200	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr17:45900600-45906200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr17:45900600-45906200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr17:45900600-45906200	Strong transcription	Spleen	Spleen
33	chr17:45900600-45906400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:45900600-45906400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr17:45900600-45906400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr17:45900600-45906400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr17:45900600-45906400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr17:45900600-45906400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr17:45900600-45906400	Strong transcription	Adipose Nuclei	Adipose
40	chr17:45900600-45906400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:45900600-45906400	Strong transcription	Placenta	Placenta
42	chr17:45900600-45906400	Strong transcription	Fetal Thymus	thymus
43	chr17:45900600-45906400	Strong transcription	Lung	lung
44	chr17:45900600-45906600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr17:45900600-45906600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:45900600-45907000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr17:45900800-45904800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr17:45900800-45904800	Strong transcription	HSMMtube	muscle
49	chr17:45900800-45905600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr17:45900800-45906000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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