Variant report

Variant	rs10411009
Chromosome Location	chr19:18606266-18606267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18604942..18607158-chr19:18631609..18633721,2	MCF-7	breast:
2	chr19:18605488..18607931-chr19:18681544..18684066,2	MCF-7	breast:
3	chr19:18586454..18593275-chr19:18604315..18608580,6	K562	blood:
4	chr19:18606016..18607670-chr19:18611209..18613492,2	MCF-7	breast:
5	chr19:18598368..18601612-chr19:18604293..18607199,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221983	Chromatin interaction
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10164319	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10403249	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405479	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10405636	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10408290	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10409003	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10409483	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10409505	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10413237	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419404	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10425982	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10427083	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1043327	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10442	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11673604	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12162221	0.92[ASN][1000 genomes]
rs12162223	0.90[ASN][1000 genomes]
rs12981981	0.92[ASN][1000 genomes]
rs1560118	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1560119	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs172032	0.92[ASN][1000 genomes]
rs1806980	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2007981	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288428	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2303695	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303696	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303697	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385088	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385089	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs271621	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs271622	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs271623	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs271624	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs271626	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs271628	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs271629	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28572537	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34010330	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34053595	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34171762	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34256197	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34746918	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3810429	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4595905	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808133	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808134	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808136	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808801	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808804	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62121135	0.92[ASN][1000 genomes]
rs7249020	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251653	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252707	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252848	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253990	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254249	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256534	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7257932	0.86[ASN][1000 genomes]
rs7258465	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs748609	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs76194	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs76195	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8100767	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8103622	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103660	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105994	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106096	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8107347	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107351	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107367	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107743	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109573	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111708	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875396	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10411009	SSBP4	cis	Esophagus Mucosa	GTEx
rs10411009	SSBP4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18575400-18607200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:18593600-18606400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr19:18594000-18621800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:18597600-18606600	Enhancers	Duodenum Mucosa	Duodenum
5	chr19:18598000-18609800	Weak transcription	Fetal Intestine Large	intestine
6	chr19:18599400-18611200	Weak transcription	Brain Germinal Matrix	brain
7	chr19:18599800-18606600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:18599800-18606800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:18599800-18611400	Weak transcription	Aorta	Aorta
10	chr19:18600200-18610400	Weak transcription	Brain Substantia Nigra	brain
11	chr19:18600200-18611400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr19:18600400-18609200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:18600400-18630600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:18600600-18607000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:18600600-18611400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr19:18600600-18619800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:18601200-18606800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr19:18601600-18606800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr19:18601800-18606600	Weak transcription	Brain Anterior Caudate	brain
20	chr19:18602200-18621400	Enhancers	Right Ventricle	heart
21	chr19:18602400-18608600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr19:18602600-18607000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr19:18602600-18621400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr19:18602800-18607400	Enhancers	Ovary	ovary
25	chr19:18602800-18607600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:18602800-18608200	Enhancers	Left Ventricle	heart
27	chr19:18602800-18608400	Enhancers	Lung	lung
28	chr19:18602800-18612600	Enhancers	Placenta	Placenta
29	chr19:18603000-18606600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr19:18603000-18608200	Enhancers	Esophagus	oesophagus
31	chr19:18603200-18607800	Enhancers	Stomach Smooth Muscle	stomach
32	chr19:18603400-18607000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr19:18603600-18607600	Enhancers	Fetal Muscle Leg	muscle
34	chr19:18603600-18607800	Enhancers	Right Atrium	heart
35	chr19:18603600-18608400	Enhancers	HepG2	liver
36	chr19:18603600-18622600	Enhancers	Psoas Muscle	Psoas
37	chr19:18603800-18608000	Enhancers	Adipose Nuclei	Adipose
38	chr19:18603800-18608200	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr19:18604000-18606400	Enhancers	Fetal Muscle Trunk	muscle
40	chr19:18604000-18607200	Weak transcription	Fetal Kidney	kidney
41	chr19:18604000-18608400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:18604000-18608600	Enhancers	Liver	Liver
43	chr19:18604000-18608800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr19:18604200-18606600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr19:18604200-18607600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr19:18604200-18610600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:18604200-18619000	Enhancers	Fetal Thymus	thymus
48	chr19:18604400-18606400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:18604400-18607000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:18604400-18607800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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