Variant report

Variant	rs10409505
Chromosome Location	chr19:18590251-18590252
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr19:18589348-18590297	IMR90	lung:	n/a	n/a
2	ELF1	chr19:18589495-18590281	HCT-116	colon:	n/a	chr19:18589842-18589853 chr19:18589841-18589854 chr19:18589842-18589853 chr19:18589858-18589869 chr19:18589843-18589852 chr19:18589904-18589917 chr19:18589857-18589870
3	HCFC1	chr19:18589553-18590255	Hela-S3	cervix:	n/a	n/a
4	MAZ	chr19:18589464-18590298	IMR90	lung:	n/a	n/a
5	MAX	chr19:18589122-18590273	HepG2	liver:	n/a	chr19:18589171-18589182
6	JUN	chr19:18588922-18590313	K562	blood:	n/a	n/a
7	RCOR1	chr19:18589552-18590327	IMR90	lung:	n/a	n/a
8	CEBPB	chr19:18589494-18590265	A549	lung:	n/a	chr19:18589867-18589884
9	MAX	chr19:18589321-18590273	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18588633..18591403-chr19:18594095..18597353,4	MCF-7	breast:
2	chr19:18578188..18581023-chr19:18588247..18591151,3	MCF-7	breast:
3	chr19:18588521..18591336-chr19:18703745..18705806,2	MCF-7	breast:
4	chr19:18589828..18592704-chr19:18699661..18702189,2	MCF-7	breast:
5	chr19:18588377..18591761-chr19:18697769..18700199,3	K562	blood:
6	chr19:18580167..18582831-chr19:18590053..18592276,2	K562	blood:
7	chr19:18585936..18588927-chr19:18589228..18592220,4	K562	blood:
8	chr19:18588554..18591195-chr19:18630663..18634025,3	MCF-7	breast:
9	chr19:18575653..18580587-chr19:18588169..18591423,6	K562	blood:

Variant related genes	Relation type
ELL	TF binding region
ENSG00000105656	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000006016	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10164319	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10403249	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10405479	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10405636	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10408290	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10409003	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10409483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411009	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10413237	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10419404	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425982	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427083	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1043327	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10442	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11673604	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12162221	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12162223	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12981981	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1560118	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1560119	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs172032	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1806980	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2007981	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288428	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303695	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303696	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2303697	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2385088	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2385089	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs271621	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs271622	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs271623	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs271624	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs271626	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs271628	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs271629	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28572537	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34010330	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34053595	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34171762	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34256197	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34509804	0.81[EUR][1000 genomes]
rs34746918	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3810429	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4595905	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808133	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808134	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808136	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808801	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808804	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121135	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7249020	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7251653	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252707	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252848	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253990	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256534	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257932	0.86[ASN][1000 genomes]
rs7258465	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs748609	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs76194	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs76195	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8100767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103622	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8103660	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105994	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8106096	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107347	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107351	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107367	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8107743	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8109573	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111708	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs875396	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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
rs10409505	SSBP4	cis	Skin Sun Exposed Lower leg	GTEx
rs10409505	SSBP4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18572600-18592400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:18575400-18607200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:18575800-18590800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:18576200-18590800	Weak transcription	Aorta	Aorta
5	chr19:18576800-18591000	Weak transcription	Fetal Brain Female	brain
6	chr19:18581400-18595600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:18581600-18597000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:18583400-18592400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:18583800-18590800	Enhancers	Duodenum Mucosa	Duodenum
10	chr19:18583800-18592600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr19:18584000-18592000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr19:18584000-18592400	Enhancers	Right Ventricle	heart
13	chr19:18584000-18592800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr19:18584200-18591800	Enhancers	Fetal Muscle Trunk	muscle
15	chr19:18584200-18592400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:18584800-18591000	Weak transcription	Fetal Brain Male	brain
17	chr19:18584800-18591600	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr19:18584800-18592000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr19:18584800-18592600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:18585000-18592400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr19:18585200-18597000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr19:18585800-18599800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr19:18586200-18592600	Enhancers	Brain Hippocampus Middle	brain
24	chr19:18586400-18591200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr19:18586400-18592000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr19:18586400-18592400	Enhancers	Adipose Nuclei	Adipose
27	chr19:18586600-18590800	Weak transcription	Fetal Heart	heart
28	chr19:18586600-18592000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:18586600-18592000	Enhancers	Liver	Liver
30	chr19:18586600-18592000	Enhancers	Left Ventricle	heart
31	chr19:18587000-18591000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:18587000-18591000	Weak transcription	Brain Germinal Matrix	brain
33	chr19:18587800-18592000	Enhancers	Esophagus	oesophagus
34	chr19:18588000-18590600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr19:18588000-18591000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:18588000-18592200	Enhancers	Primary B cells from cord blood	blood
37	chr19:18588200-18590600	Enhancers	Stomach Smooth Muscle	stomach
38	chr19:18588200-18591400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:18588200-18592200	Enhancers	Fetal Muscle Leg	muscle
40	chr19:18588200-18593000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr19:18588200-18598200	Enhancers	Spleen	Spleen
42	chr19:18588400-18590800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:18588400-18591600	Enhancers	HSMMtube	muscle
44	chr19:18588400-18592000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:18588600-18590600	Weak transcription	Brain Angular Gyrus	brain
46	chr19:18588600-18591200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr19:18588600-18591600	Enhancers	Right Atrium	heart
48	chr19:18588600-18592600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:18588600-18592600	Enhancers	Psoas Muscle	Psoas
50	chr19:18588600-18593400	Enhancers	K562	blood

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