Variant report

Variant	rs3909258
Chromosome Location	chr17:19945819-19945820
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19945642..19947610-chr17:19953431..19955992,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10083856	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1034904	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11867585	0.84[AMR][1000 genomes]
rs11868084	0.81[AMR][1000 genomes]
rs11869616	0.81[AMR][1000 genomes]
rs11870111	0.81[AMR][1000 genomes]
rs11871651	0.86[AMR][1000 genomes]
rs16960644	0.91[ASN][1000 genomes]
rs1860302	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2108979	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108980	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28603224	0.84[AMR][1000 genomes]
rs28637614	0.84[AMR][1000 genomes]
rs28666381	0.84[AMR][1000 genomes]
rs28807825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34290687	0.83[AMR][1000 genomes]
rs34291370	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34401389	0.83[AMR][1000 genomes]
rs35003563	0.83[AMR][1000 genomes]
rs36034566	0.80[EUR][1000 genomes]
rs36077949	0.84[AMR][1000 genomes]
rs3862152	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3888318	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4005937	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4267380	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4479308	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4479309	0.85[AMR][1000 genomes]
rs4570919	0.85[AMR][1000 genomes]
rs4924801	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924803	0.83[AMR][1000 genomes]
rs4924806	0.85[AMR][1000 genomes]
rs4925065	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925066	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925067	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925069	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925072	0.88[AMR][1000 genomes]
rs4925073	0.87[AMR][1000 genomes]
rs4925077	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4925079	0.84[AMR][1000 genomes]
rs4925081	0.83[AMR][1000 genomes]
rs4925085	0.82[AMR][1000 genomes]
rs56142708	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62067555	0.85[AMR][1000 genomes]
rs7207625	0.85[AMR][1000 genomes]
rs7208025	0.85[AMR][1000 genomes]
rs7208365	0.85[AMR][1000 genomes]
rs7208635	0.85[AMR][1000 genomes]
rs7209734	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7211535	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7218708	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7223305	0.85[AMR][1000 genomes]
rs8065337	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8067545	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs888423	0.85[AMR][1000 genomes]
rs918227	0.80[AMR][1000 genomes]
rs918228	0.85[AMR][1000 genomes]
rs9889743	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9891739	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896411	0.84[AMR][1000 genomes]
rs9897246	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9897653	0.83[AMR][1000 genomes]
rs9906625	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9907788	0.87[AMR][1000 genomes]
rs9909009	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9912775	0.83[AMR][1000 genomes]
rs9915758	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9944451	0.85[AMR][1000 genomes]

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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3909258	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19923400-19956600	Weak transcription	A549	lung
2	chr17:19923600-19946400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr17:19926400-19947000	Weak transcription	Brain Angular Gyrus	brain
4	chr17:19932000-19956800	Weak transcription	Ovary	ovary
5	chr17:19936200-19946200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:19941000-19946400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr17:19942800-19950400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr17:19943800-19965800	Weak transcription	Aorta	Aorta
9	chr17:19944000-19947200	Weak transcription	Brain Substantia Nigra	brain
10	chr17:19944000-19950000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:19944400-19946600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr17:19945400-19947000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:19945600-19946000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr17:19945600-19946400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr17:19945600-19946800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:19945600-19947000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr17:19945800-19956000	Weak transcription	K562	blood

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