Variant report

Variant	rs35939822
Chromosome Location	chr19:40033914-40033915
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39925244..39927347-chr19:40032319..40034219,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SELV.1-4	chr19:40033410-40034013	l_1683_chr19:40024566-40034013_testes

Variant related genes	Relation type
ENSG00000196235	Chromatin interaction
ENSG00000105193	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12608773	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12610740	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12610751	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12610833	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12611125	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12972285	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12972675	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12973775	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12980249	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17795475	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34271968	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34856311	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34885802	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35038530	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3746086	0.88[ASN][1000 genomes]
rs4803258	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4803259	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55994613	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59485553	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60587381	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247184	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247218	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7257553	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7257904	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258348	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40031000-40037200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:40031200-40034800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:40031200-40043600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:40031200-40049600	Weak transcription	Right Atrium	heart
5	chr19:40031400-40034000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:40031400-40034200	Weak transcription	Primary T cells from cord blood	blood
7	chr19:40031400-40034200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:40031400-40034800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:40031400-40042200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:40031600-40034000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:40031600-40034200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:40032600-40038000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr19:40032800-40035200	Enhancers	HMEC	breast
14	chr19:40032800-40035400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:40032800-40035400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:40032800-40035600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:40032800-40035800	Enhancers	NHEK	skin
18	chr19:40032800-40036200	Enhancers	Placenta	Placenta
19	chr19:40032800-40038000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr19:40033200-40034000	Enhancers	Primary hematopoietic stem cells	blood
21	chr19:40033400-40036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:40033600-40042200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:40033800-40034000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:40033800-40034200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr19:40033800-40035000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr19:40033800-40035400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:40033800-40035600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr19:40033800-40038000	Enhancers	Primary T cells fromperipheralblood	blood

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