Variant report

Variant	rs10423802
Chromosome Location	chr19:18567901-18567902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18562074..18564464-chr19:18567601..18569747,2	K562	blood:
2	chr19:18567052..18568764-chr19:18574029..18576379,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10402322	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10409346	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10409408	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10410797	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10413922	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10416993	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10418331	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10418554	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420384	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426768	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1045631	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11086110	0.86[EUR][1000 genomes]
rs11668704	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11670392	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11672385	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11879757	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980726	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982295	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12983263	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1469412	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1469413	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1971093	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013069	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162797	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303692	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28534973	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891676	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34213500	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35004712	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35742476	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4006662	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4303657	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4580317	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808135	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808802	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808803	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808805	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808806	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808807	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808808	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808811	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808812	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808813	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55715336	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57923655	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6512268	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6512269	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6512270	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6512271	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7246788	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247540	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249760	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252130	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7252185	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7255936	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7256530	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7258891	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7259135	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7507218	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8100343	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8102717	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104247	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106068	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8106332	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8111397	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111582	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111824	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8112372	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8112859	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs888668	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888669	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10423802	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10423802	SSBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18545200-18570000	Weak transcription	Small Intestine	intestine
2	chr19:18550800-18569800	Weak transcription	Right Atrium	heart
3	chr19:18551600-18570600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:18553400-18579000	Weak transcription	Fetal Kidney	kidney
5	chr19:18553800-18578000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:18554000-18577600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:18556800-18574800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:18557600-18569000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:18559200-18568600	Weak transcription	K562	blood
10	chr19:18559400-18568600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:18561600-18570200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:18561600-18570600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr19:18561800-18571000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:18561800-18571000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:18562200-18570800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:18562200-18571000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:18562200-18580200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:18562200-18580600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:18562400-18568200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr19:18562400-18568800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr19:18562400-18571800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:18562600-18569000	Weak transcription	Stomach Mucosa	stomach
23	chr19:18562600-18569400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:18562600-18569800	Strong transcription	Fetal Intestine Small	intestine
25	chr19:18562600-18571000	Weak transcription	Aorta	Aorta
26	chr19:18562800-18580800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr19:18564000-18568200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:18564600-18568200	Weak transcription	HSMMtube	muscle
29	chr19:18565000-18568600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:18565000-18568600	Weak transcription	NH-A	brain
31	chr19:18565000-18570000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:18565000-18570800	Weak transcription	A549	lung
33	chr19:18565200-18568400	Weak transcription	Hela-S3	cervix
34	chr19:18566000-18568000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:18566000-18574400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:18566200-18568000	Strong transcription	Lung	lung
37	chr19:18566200-18570000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:18566200-18572600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr19:18566200-18574000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:18566200-18574000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:18566400-18568400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:18566400-18568400	Strong transcription	Brain Germinal Matrix	brain
43	chr19:18566400-18568800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:18566400-18569600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr19:18566400-18570000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:18566400-18570000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr19:18566400-18572800	Strong transcription	Primary T cells from cord blood	blood
48	chr19:18566400-18572800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:18566400-18575600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr19:18566400-18575800	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links