Variant report

Variant	rs10405479
Chromosome Location	chr19:18563880-18563881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18562199..18564627-chr19:18631303..18633445,2	MCF-7	breast:
2	chr19:18562074..18564464-chr19:18567601..18569747,2	K562	blood:

Variant related genes	Relation type
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10164319	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403249	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10405636	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10408290	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409003	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409483	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10409505	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10411009	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10413237	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10419404	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10425982	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10427083	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1043327	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10442	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11673604	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12162221	0.86[ASN][1000 genomes]
rs12162223	0.85[ASN][1000 genomes]
rs12981981	0.86[ASN][1000 genomes]
rs1560118	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560119	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs172032	0.86[ASN][1000 genomes]
rs1806980	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2007981	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288428	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303695	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303696	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2303697	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385088	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385089	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs271621	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs271622	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs271623	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs271624	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs271626	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs271628	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs271629	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28375303	0.84[ASN][1000 genomes]
rs28572537	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34010330	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34053595	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34171762	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34256197	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34509804	0.83[ASN][1000 genomes]
rs34746918	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3810429	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4595905	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808133	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808134	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808136	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808801	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808804	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62121135	0.86[ASN][1000 genomes]
rs7249020	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7251653	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7252707	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7252848	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7253990	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254249	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256534	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257932	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7258465	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs748609	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs76194	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs76195	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8100767	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8103622	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103660	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105994	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106096	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107347	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107351	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107367	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107743	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109573	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111708	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875396	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking 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	162 gene(s)	inside rSNPs	diseases
3	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
7	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
8	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
9	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10405479	SSBP4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18545200-18570000	Weak transcription	Small Intestine	intestine
2	chr19:18549200-18566200	Weak transcription	HUVEC	blood vessel
3	chr19:18549800-18567000	Weak transcription	Psoas Muscle	Psoas
4	chr19:18550800-18569800	Weak transcription	Right Atrium	heart
5	chr19:18551600-18570600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:18553400-18564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:18553400-18564800	Strong transcription	Lung	lung
8	chr19:18553400-18579000	Weak transcription	Fetal Kidney	kidney
9	chr19:18553600-18564200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:18553600-18564200	Strong transcription	NHEK	skin
11	chr19:18553600-18565000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr19:18553800-18565000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:18553800-18565400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr19:18553800-18578000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:18554000-18577600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:18554200-18564000	Strong transcription	Primary T cells from cord blood	blood
17	chr19:18554200-18565000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:18556800-18574800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr19:18557600-18569000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr19:18559200-18568600	Weak transcription	K562	blood
21	chr19:18559400-18568600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:18560400-18567000	Weak transcription	HSMM	muscle
23	chr19:18561000-18566000	Genic enhancers	Placenta	Placenta
24	chr19:18561200-18564600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr19:18561400-18566400	Weak transcription	Brain Germinal Matrix	brain
26	chr19:18561400-18567000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr19:18561600-18564200	Weak transcription	HMEC	breast
28	chr19:18561600-18564800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:18561600-18567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:18561600-18570200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:18561600-18570600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:18561800-18564000	Weak transcription	NH-A	brain
33	chr19:18561800-18566800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:18561800-18567000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:18561800-18571000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:18561800-18571000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:18562000-18564200	Enhancers	Hela-S3	cervix
38	chr19:18562000-18564800	Enhancers	NHDF-Ad	bronchial
39	chr19:18562000-18565000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr19:18562200-18566600	Weak transcription	Ovary	ovary
41	chr19:18562200-18570800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr19:18562200-18571000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:18562200-18580200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr19:18562200-18580600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:18562400-18564000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:18562400-18564000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:18562400-18564000	Weak transcription	Brain Substantia Nigra	brain
48	chr19:18562400-18564000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:18562400-18564200	Strong transcription	Fetal Thymus	thymus
50	chr19:18562400-18564200	Weak transcription	A549	lung

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