Variant report

Variant	rs7246788
Chromosome Location	chr19:18575450-18575451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18573630..18576547-chr19:18700446..18702427,2	K562	blood:
2	chr19:18568659..18571557-chr19:18575200..18577928,3	K562	blood:
3	chr19:18539549..18542308-chr19:18573841..18576282,3	K562	blood:
4	chr19:18546700..18549540-chr19:18575165..18577449,2	MCF-7	breast:
5	chr19:18574479..18576358-chr19:18579321..18581431,3	K562	blood:
6	chr19:18567052..18568764-chr19:18574029..18576379,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006015	Chromatin interaction
ENSG00000105655	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10164323	0.86[JPT][hapmap]
rs10402322	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10409346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10409408	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10410797	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10413922	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10416993	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10418331	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10418554	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10420384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10423802	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10426768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045631	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11086110	0.87[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs11668704	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11672385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11879757	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12980726	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12982295	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12983263	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1469412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1469413	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2013069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2162797	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303692	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28534973	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2891676	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34213500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35004712	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35742476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4006662	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4303657	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4580317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808802	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808803	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808805	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808808	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808811	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808813	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55715336	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57923655	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6512268	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6512269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6512270	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6512271	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247540	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251640	1.00[CHB][hapmap]
rs7252130	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7252185	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7255936	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7256530	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7258891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7259135	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7507218	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8100343	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8102717	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104247	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8106068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8106332	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8111397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111582	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8112372	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8112859	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs888668	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs888669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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	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	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
7	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
8	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
9	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
rs7246788	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs7246788	SSBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18553400-18579000	Weak transcription	Fetal Kidney	kidney
2	chr19:18553800-18578000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr19:18554000-18577600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:18562200-18580200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:18562200-18580600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:18562800-18580800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:18566400-18575600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr19:18566400-18575800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr19:18566600-18575600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:18566800-18577200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr19:18566800-18577600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr19:18567000-18575800	Strong transcription	Thymus	Thymus
13	chr19:18567000-18577400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr19:18567800-18578200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:18568200-18583800	Weak transcription	Fetal Brain Male	brain
16	chr19:18571200-18576600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:18571400-18584200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:18571800-18581200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:18571800-18589600	Weak transcription	HUVEC	blood vessel
20	chr19:18572200-18581000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:18572200-18589600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:18572400-18575800	Weak transcription	Aorta	Aorta
23	chr19:18572400-18581200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:18572400-18583200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:18572600-18575600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:18572600-18575800	Weak transcription	HMEC	breast
27	chr19:18572600-18580600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:18572600-18581000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:18572600-18581200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr19:18572600-18592400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:18572800-18575600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:18572800-18576800	Weak transcription	Fetal Heart	heart
33	chr19:18572800-18578000	Weak transcription	HSMM	muscle
34	chr19:18573200-18575600	Weak transcription	K562	blood
35	chr19:18573400-18577800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr19:18573800-18575600	Weak transcription	Colonic Mucosa	Colon
37	chr19:18574000-18575600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:18574000-18575600	Weak transcription	Gastric	stomach
39	chr19:18574000-18575800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr19:18574400-18575600	Enhancers	Brain Cingulate Gyrus	brain
41	chr19:18574400-18577400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:18574600-18576800	Strong transcription	Fetal Brain Female	brain
43	chr19:18574600-18577200	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr19:18574600-18577400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:18574800-18575600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:18574800-18575800	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr19:18574800-18575800	Enhancers	Rectal Smooth Muscle	rectum
48	chr19:18574800-18575800	Enhancers	NHLF	lung
49	chr19:18574800-18576000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:18574800-18576400	Genic enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links