Variant report

Variant	rs1560118
Chromosome Location	chr19:18570035-18570036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18568659..18571557-chr19:18575200..18577928,3	K562	blood:
2	chr19:18495359..18498345-chr19:18569235..18570904,2	K562	blood:
3	chr19:18570000..18571502-chr19:18652143..18654707,2	K562	blood:
4	chr19:18557716..18560306-chr19:18569025..18571583,2	K562	blood:

Variant related genes	Relation type
ENSG00000130513	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000105701	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10164319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10164323	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10403249	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10405479	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10408290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409003	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409483	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10409505	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10411009	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10413237	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10419404	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10420384	0.82[JPT][hapmap]
rs10425982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10427083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1043327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11673604	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.89[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]
rs1560119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs172032	0.86[ASN][1000 genomes]
rs1806980	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2007981	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2288428	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303696	0.92[ASN][1000 genomes]
rs2303697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs271621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs271622	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs271623	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs271624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs271626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs271628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs271629	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28375303	0.84[ASN][1000 genomes]
rs28572537	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34010330	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34053595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34171762	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34256197	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34509804	0.83[ASN][1000 genomes]
rs34746918	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3810429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4595905	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808133	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808134	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808136	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808804	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62121135	0.86[ASN][1000 genomes]
rs7249020	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7251653	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7252707	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7252848	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7253990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254249	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257932	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7258465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs748609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs76194	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs76195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8100767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8103622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103660	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106096	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107347	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107351	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107367	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107743	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109573	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111708	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[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
rs1560118	SSBP4	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18551600-18570600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:18553400-18579000	Weak transcription	Fetal Kidney	kidney
3	chr19:18553800-18578000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr19:18554000-18577600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:18556800-18574800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:18561600-18570200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr19:18561600-18570600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:18561800-18571000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:18561800-18571000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:18562200-18570800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr19:18562200-18571000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:18562200-18580200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:18562200-18580600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:18562400-18571800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:18562600-18571000	Weak transcription	Aorta	Aorta
16	chr19:18562800-18580800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr19:18565000-18570800	Weak transcription	A549	lung
18	chr19:18566000-18574400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:18566200-18572600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr19:18566200-18574000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:18566200-18574000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:18566400-18572800	Strong transcription	Primary T cells from cord blood	blood
23	chr19:18566400-18572800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:18566400-18575600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr19:18566400-18575800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr19:18566600-18571000	Strong transcription	Liver	Liver
27	chr19:18566600-18572600	Strong transcription	GM12878-XiMat	blood
28	chr19:18566600-18572800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:18566600-18575600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:18566800-18570200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
31	chr19:18566800-18570200	Strong transcription	HMEC	breast
32	chr19:18566800-18570600	Strong transcription	Esophagus	oesophagus
33	chr19:18566800-18570800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr19:18566800-18572600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:18566800-18572800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:18566800-18573800	Strong transcription	Primary B cells from cord blood	blood
37	chr19:18566800-18574000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:18566800-18575000	Strong transcription	HepG2	liver
39	chr19:18566800-18577200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr19:18566800-18577600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr19:18567000-18570200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr19:18567000-18570200	Strong transcription	NHEK	skin
43	chr19:18567000-18570600	Weak transcription	HUVEC	blood vessel
44	chr19:18567000-18570800	Strong transcription	Gastric	stomach
45	chr19:18567000-18571000	Strong transcription	Fetal Thymus	thymus
46	chr19:18567000-18571000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:18567000-18572600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:18567000-18572600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:18567000-18573800	Genic enhancers	Placenta	Placenta
50	chr19:18567000-18573800	Strong transcription	Dnd41	blood

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