Variant report

Variant	rs7259135
Chromosome Location	chr19:18593153-18593154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18591779..18593925-chr19:18596031..18599747,3	MCF-7	breast:
2	chr19:18590783..18593935-chr19:18596275..18598325,3	K562	blood:
3	chr19:18590783..18594037-chr19:18595527..18599240,6	K562	blood:
4	chr19:18586856..18589889-chr19:18592083..18594396,3	K562	blood:
5	chr19:18590797..18594218-chr19:18631052..18634503,4	MCF-7	breast:
6	chr19:18591373..18594361-chr19:18652697..18655372,2	K562	blood:

Variant related genes	Relation type
ENSG00000105701	Chromatin interaction
ENSG00000105656	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	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10409346	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10409408	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10410797	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10413922	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10416993	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10418331	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10418554	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420384	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10423802	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10426768	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1045631	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11668704	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670392	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672385	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11879757	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12980726	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12982295	0.84[ASN][1000 genomes]
rs12983263	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1469412	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469413	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1971093	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013069	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2162797	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303692	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28534973	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2891676	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34213500	0.83[ASN][1000 genomes]
rs35004712	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35742476	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4006662	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4303657	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4580317	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808135	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808802	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808803	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808805	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808806	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808807	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808808	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808811	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808812	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808813	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55715336	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57923655	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6512268	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6512269	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6512270	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6512271	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7246788	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247540	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7249760	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7251232	0.80[EUR][1000 genomes]
rs7252130	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7252185	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7255936	0.87[ASN][1000 genomes]
rs7256530	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7258891	0.83[ASN][1000 genomes]
rs7507218	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8100343	0.84[ASN][1000 genomes]
rs8102717	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104247	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106068	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8106332	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111397	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8111582	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8111824	0.83[ASN][1000 genomes]
rs8112372	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8112859	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs888668	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs888669	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[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
rs7259135	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs7259135	SSBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 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	chr19:18581400-18595600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:18581600-18597000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:18585200-18597000	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr19:18585800-18599800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr19:18588200-18598200	Enhancers	Spleen	Spleen
7	chr19:18588600-18593400	Enhancers	K562	blood
8	chr19:18589000-18593200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:18590000-18596800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:18590800-18596000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:18591000-18605400	Weak transcription	Thymus	Thymus
12	chr19:18591200-18594800	Enhancers	Osteobl	bone
13	chr19:18591200-18596000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr19:18591400-18593400	Enhancers	Colon Smooth Muscle	Colon
15	chr19:18591400-18593800	Weak transcription	Brain Anterior Caudate	brain
16	chr19:18591400-18594000	Weak transcription	Fetal Brain Female	brain
17	chr19:18591400-18594000	Weak transcription	NHEK	skin
18	chr19:18591400-18594200	Weak transcription	HepG2	liver
19	chr19:18591400-18594200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr19:18591400-18594600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:18591400-18594600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:18591400-18595800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:18591400-18595800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:18591400-18595800	Weak transcription	Ovary	ovary
25	chr19:18591400-18596200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:18591400-18596800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:18591400-18596800	Weak transcription	Brain Substantia Nigra	brain
28	chr19:18591400-18596800	Weak transcription	Fetal Heart	heart
29	chr19:18591400-18596800	Weak transcription	A549	lung
30	chr19:18591400-18597000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr19:18591400-18597400	Weak transcription	Aorta	Aorta
32	chr19:18591400-18605200	Weak transcription	Primary T cells from cord blood	blood
33	chr19:18591400-18605400	Weak transcription	GM12878-XiMat	blood
34	chr19:18591600-18593600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:18591600-18593800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:18591600-18593800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:18591600-18593800	Weak transcription	HSMMtube	muscle
38	chr19:18591600-18594000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr19:18591600-18594000	Weak transcription	Right Atrium	heart
40	chr19:18591600-18596000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr19:18591600-18597000	Weak transcription	Brain Angular Gyrus	brain
42	chr19:18591600-18597000	Weak transcription	Fetal Lung	lung
43	chr19:18591800-18593600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:18591800-18594000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:18591800-18594000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:18591800-18595200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:18591800-18597000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:18592000-18593600	Weak transcription	Left Ventricle	heart
49	chr19:18592000-18593600	Weak transcription	HSMM	muscle
50	chr19:18592000-18593800	Weak transcription	Liver	Liver

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