Variant report

Variant	rs10416993
Chromosome Location	chr19:18600455-18600456
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18596615..18599605-chr19:18599689..18601535,3	K562	blood:
2	chr19:18599219..18600750-chr19:18614089..18616331,2	MCF-7	breast:
3	chr19:18599505..18602337-chr19:18612086..18613638,2	MCF-7	breast:
4	chr19:18578145..18580675-chr19:18600107..18604361,3	MCF-7	breast:
5	chr19:18597781..18601216-chr19:18667431..18670376,3	MCF-7	breast:
6	chr19:18594286..18597312-chr19:18598721..18600664,3	K562	blood:
7	chr19:18600195..18604432-chr19:18699323..18701872,3	K562	blood:
8	chr19:18594916..18600646-chr19:18631140..18634129,11	MCF-7	breast:
9	chr19:18581749..18584173-chr19:18598767..18601257,2	K562	blood:
10	chr19:18597905..18599605-chr19:18599689..18601535,2	K562	blood:
11	chr19:18598368..18601612-chr19:18604293..18607199,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105656	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000105700	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10402322	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10409346	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10409408	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10410797	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10413922	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10418331	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10418554	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420384	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10423802	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10426768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1045631	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11086110	0.85[EUR][1000 genomes]
rs11668704	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11670392	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11672385	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11879757	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12980726	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12982295	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12983263	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1469412	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469413	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1971093	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2013069	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2162797	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303692	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28534973	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2891676	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34213500	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35004712	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35742476	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4006662	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4303657	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4580317	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808135	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808802	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808803	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808805	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808806	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808807	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808808	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808811	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808812	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808813	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55715336	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57923655	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6512268	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512269	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6512270	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6512271	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246788	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247540	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7249760	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252130	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7252185	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255936	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7256530	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258891	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7259135	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7507218	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8100343	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8102717	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8104247	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8106068	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106332	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8111397	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8111582	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8111824	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8112372	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8112859	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs888668	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs888669	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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
rs10416993	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10416993	SSBP4	Cis_1M	lymphoblastoid	RTeQTL

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	chr19:18591000-18605400	Weak transcription	Thymus	Thymus
3	chr19:18591400-18605200	Weak transcription	Primary T cells from cord blood	blood
4	chr19:18591400-18605400	Weak transcription	GM12878-XiMat	blood
5	chr19:18593600-18606400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr19:18593800-18601600	Enhancers	Liver	Liver
7	chr19:18594000-18601800	Enhancers	Lung	lung
8	chr19:18594000-18605000	Enhancers	Pancreas	Pancrea
9	chr19:18594000-18621800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:18594200-18601600	Enhancers	Placenta	Placenta
11	chr19:18594600-18605600	Weak transcription	Fetal Brain Female	brain
12	chr19:18595200-18600600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:18595200-18600800	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr19:18595400-18601800	Enhancers	Left Ventricle	heart
15	chr19:18595400-18605800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr19:18595600-18601600	Enhancers	Psoas Muscle	Psoas
17	chr19:18595600-18601800	Enhancers	Right Ventricle	heart
18	chr19:18596000-18601200	Enhancers	Right Atrium	heart
19	chr19:18596000-18601400	Enhancers	Fetal Thymus	thymus
20	chr19:18596200-18601200	Enhancers	Brain Anterior Caudate	brain
21	chr19:18597000-18600600	Enhancers	HMEC	breast
22	chr19:18597000-18600800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:18597200-18601000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr19:18597200-18601800	Enhancers	Fetal Muscle Leg	muscle
25	chr19:18597400-18600800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:18597400-18603800	Weak transcription	Fetal Kidney	kidney
27	chr19:18597600-18602000	Enhancers	K562	blood
28	chr19:18597600-18606600	Enhancers	Duodenum Mucosa	Duodenum
29	chr19:18597800-18603800	Weak transcription	Fetal Lung	lung
30	chr19:18597800-18604400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:18597800-18604400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:18597800-18605400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:18598000-18601200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:18598000-18603400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:18598000-18604400	Weak transcription	NHLF	lung
36	chr19:18598000-18605200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr19:18598000-18609800	Weak transcription	Fetal Intestine Large	intestine
38	chr19:18598200-18600800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr19:18598200-18605400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr19:18598400-18600800	Enhancers	Gastric	stomach
41	chr19:18598400-18604200	Weak transcription	Small Intestine	intestine
42	chr19:18598600-18600600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:18598600-18600600	Enhancers	Brain Hippocampus Middle	brain
44	chr19:18598600-18600600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr19:18598600-18603800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:18598800-18600600	Enhancers	A549	lung
47	chr19:18598800-18605400	Weak transcription	Primary B cells from cord blood	blood
48	chr19:18599000-18600800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr19:18599000-18600800	Enhancers	Fetal Heart	heart
50	chr19:18599000-18602000	Enhancers	Primary T helper cells fromperipheralblood	blood

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