Variant report

Variant	rs7254249
Chromosome Location	chr19:18591745-18591746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18590783..18593935-chr19:18596275..18598325,3	K562	blood:
2	chr19:18589828..18592704-chr19:18699661..18702189,2	MCF-7	breast:
3	chr19:18588377..18591761-chr19:18697769..18700199,3	K562	blood:
4	chr19:18580167..18582831-chr19:18590053..18592276,2	K562	blood:
5	chr19:18590783..18594037-chr19:18595527..18599240,6	K562	blood:
6	chr19:18585936..18588927-chr19:18589228..18592220,4	K562	blood:
7	chr19:18558483..18560540-chr19:18590272..18592591,2	MCF-7	breast:
8	chr19:18590797..18594218-chr19:18631052..18634503,4	MCF-7	breast:
9	chr19:18591373..18594361-chr19:18652697..18655372,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105701	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000006015	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]
rs10409505	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]
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
rs7254249	SSBP4	cis	Skin Sun Exposed Lower leg	GTEx
rs7254249	SSBP4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:110 , 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	chr19:18581400-18595600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:18581600-18597000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:18583400-18592400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:18583800-18592600	Enhancers	Primary T cells fromperipheralblood	blood
7	chr19:18584000-18592000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr19:18584000-18592400	Enhancers	Right Ventricle	heart
9	chr19:18584000-18592800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr19:18584200-18591800	Enhancers	Fetal Muscle Trunk	muscle
11	chr19:18584200-18592400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:18584800-18592000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr19:18584800-18592600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:18585000-18592400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr19:18585200-18597000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr19:18585800-18599800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr19:18586200-18592600	Enhancers	Brain Hippocampus Middle	brain
18	chr19:18586400-18592000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr19:18586400-18592400	Enhancers	Adipose Nuclei	Adipose
20	chr19:18586600-18592000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:18586600-18592000	Enhancers	Liver	Liver
22	chr19:18586600-18592000	Enhancers	Left Ventricle	heart
23	chr19:18587800-18592000	Enhancers	Esophagus	oesophagus
24	chr19:18588000-18592200	Enhancers	Primary B cells from cord blood	blood
25	chr19:18588200-18592200	Enhancers	Fetal Muscle Leg	muscle
26	chr19:18588200-18593000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr19:18588200-18598200	Enhancers	Spleen	Spleen
28	chr19:18588400-18592000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:18588600-18592600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:18588600-18592600	Enhancers	Psoas Muscle	Psoas
31	chr19:18588600-18593400	Enhancers	K562	blood
32	chr19:18588800-18592200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr19:18588800-18592400	Enhancers	Gastric	stomach
34	chr19:18588800-18592400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr19:18588800-18592600	Enhancers	Pancreas	Pancrea
36	chr19:18588800-18593000	Enhancers	Lung	lung
37	chr19:18588800-18593000	Enhancers	HMEC	breast
38	chr19:18589000-18592400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr19:18589000-18592600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr19:18589000-18593200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:18589200-18591800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:18589200-18592000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:18589200-18592200	Enhancers	Fetal Thymus	thymus
44	chr19:18589200-18592600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr19:18589400-18591800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:18589400-18592000	Enhancers	Stomach Mucosa	stomach
47	chr19:18589400-18592200	Enhancers	Fetal Intestine Large	intestine
48	chr19:18589400-18592400	Enhancers	NHLF	lung
49	chr19:18589400-18592600	Enhancers	NHDF-Ad	bronchial
50	chr19:18589400-18593000	Enhancers	NH-A	brain

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