Variant report

Variant	rs10426768
Chromosome Location	chr19:18589361-18589362
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr19:18589333-18590084	HepG2	liver:	n/a	chr19:18589541-18589556 chr19:18589541-18589549 chr19:18589541-18589556
2	MXI1	chr19:18589348-18590297	IMR90	lung:	n/a	n/a
3	HNF4A	chr19:18589323-18589712	HepG2	liver:	n/a	chr19:18589541-18589556 chr19:18589541-18589549 chr19:18589541-18589556
4	MYBL2	chr19:18589290-18590142	HepG2	liver:	n/a	n/a
5	SMARCC1	chr19:18589198-18590062	Hela-S3	cervix:	n/a	n/a
6	ELF1	chr19:18589127-18590150	GM12878	blood:	n/a	chr19:18589842-18589853 chr19:18589841-18589854 chr19:18589842-18589853 chr19:18589858-18589869 chr19:18589843-18589852 chr19:18589904-18589917 chr19:18589857-18589870
7	MAX	chr19:18589122-18590273	HepG2	liver:	n/a	chr19:18589171-18589182
8	JUN	chr19:18588922-18590313	K562	blood:	n/a	n/a
9	MAFK	chr19:18589295-18589482	HepG2	liver:	n/a	n/a
10	HNF4G	chr19:18589352-18590027	HepG2	liver:	n/a	chr19:18589541-18589556 chr19:18589541-18589549 chr19:18589541-18589556
11	TFAP2A	chr19:18589212-18590096	Hela-S3	cervix:	n/a	chr19:18589236-18589247 chr19:18589236-18589246 chr19:18589824-18589838 chr19:18589236-18589246 chr19:18589824-18589839 chr19:18589234-18589248 chr19:18589824-18589838 chr19:18589236-18589246
12	HEY1	chr19:18589355-18590081	HepG2	liver:	n/a	n/a
13	MXI1	chr19:18589308-18590108	HepG2	liver:	n/a	n/a
14	POLR2A	chr19:18588707-18590175	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:18589307-18590214	GM12892	blood:	n/a	n/a
16	MAX	chr19:18589321-18590273	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:18589337-18590188	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18588633..18591403-chr19:18594095..18597353,4	MCF-7	breast:
2	chr19:18578188..18581023-chr19:18588247..18591151,3	MCF-7	breast:
3	chr19:18588521..18591336-chr19:18703745..18705806,2	MCF-7	breast:
4	chr19:18588377..18591761-chr19:18697769..18700199,3	K562	blood:
5	chr19:18586856..18589889-chr19:18592083..18594396,3	K562	blood:
6	chr19:18585936..18588927-chr19:18589228..18592220,4	K562	blood:
7	chr19:18588554..18591195-chr19:18630663..18634025,3	MCF-7	breast:
8	chr19:18581042..18584952-chr19:18587091..18589760,3	K562	blood:
9	chr19:18575653..18580587-chr19:18588169..18591423,6	K562	blood:

Variant related genes	Relation type
ELL	TF binding region
ENSG00000006016	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10164323	0.86[JPT][hapmap]
rs10402322	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10409346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10409408	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10410797	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10413922	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10416993	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10418331	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10418554	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10420384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10423802	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];0.93[ASN][1000 genomes]
rs11086110	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes]
rs11668704	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879757	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12980726	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982295	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12983263	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469413	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1971093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2162797	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303692	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28534973	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2891676	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34213500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35004712	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35742476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4006662	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4303657	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4580317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808802	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808803	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808808	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808811	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808812	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]
rs4808813	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55715336	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57923655	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6512268	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6512269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6512270	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6512271	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246788	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]
rs7247540	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7251640	1.00[CHB][hapmap]
rs7252130	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7252185	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7255936	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7256530	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7259135	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7507218	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8100343	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8102717	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104247	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8106332	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111582	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8112372	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8112859	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs888668	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs888669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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
rs10426768	SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10426768	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18571800-18589600	Weak transcription	HUVEC	blood vessel
2	chr19:18572200-18589600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr19:18572600-18592400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:18575400-18607200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:18575800-18590800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:18576200-18590800	Weak transcription	Aorta	Aorta
7	chr19:18576400-18589600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:18576800-18591000	Weak transcription	Fetal Brain Female	brain
9	chr19:18578400-18589400	Weak transcription	NH-A	brain
10	chr19:18581000-18589800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:18581400-18595600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:18581600-18597000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:18581800-18589400	Weak transcription	NHLF	lung
14	chr19:18581800-18589600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr19:18581800-18590000	Weak transcription	Dnd41	blood
16	chr19:18582400-18589600	Weak transcription	Thymus	Thymus
17	chr19:18583400-18589600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:18583400-18592400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:18583600-18590000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:18583800-18590800	Enhancers	Duodenum Mucosa	Duodenum
21	chr19:18583800-18592600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr19:18584000-18589400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:18584000-18592000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr19:18584000-18592400	Enhancers	Right Ventricle	heart
25	chr19:18584000-18592800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr19:18584200-18591800	Enhancers	Fetal Muscle Trunk	muscle
27	chr19:18584200-18592400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:18584600-18589400	Weak transcription	HSMM	muscle
29	chr19:18584800-18591000	Weak transcription	Fetal Brain Male	brain
30	chr19:18584800-18591600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr19:18584800-18592000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr19:18584800-18592600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr19:18585000-18589800	Weak transcription	Primary T cells from cord blood	blood
34	chr19:18585000-18592400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr19:18585200-18597000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr19:18585600-18589400	Weak transcription	Small Intestine	intestine
37	chr19:18585800-18599800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr19:18586200-18592600	Enhancers	Brain Hippocampus Middle	brain
39	chr19:18586400-18589600	Enhancers	Brain Substantia Nigra	brain
40	chr19:18586400-18591200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr19:18586400-18592000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr19:18586400-18592400	Enhancers	Adipose Nuclei	Adipose
43	chr19:18586600-18590800	Weak transcription	Fetal Heart	heart
44	chr19:18586600-18592000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:18586600-18592000	Enhancers	Liver	Liver
46	chr19:18586600-18592000	Enhancers	Left Ventricle	heart
47	chr19:18586800-18589400	Enhancers	Brain Cingulate Gyrus	brain
48	chr19:18587000-18591000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:18587000-18591000	Weak transcription	Brain Germinal Matrix	brain
50	chr19:18587200-18589400	Weak transcription	Fetal Intestine Large	intestine

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