Variant report

Variant	rs1017102
Chromosome Location	chr19:56892632-56892633
allele	A/C
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	POLR2A	chr19:56891565-56892756	K562	blood:	n/a	n/a
2	POLR2A	chr19:56892511-56892643	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56892466..56895043-chr19:56896367..56898392,2	K562	blood:
2	chr19:56890954..56893451-chr19:56903592..56906297,2	K562	blood:

Variant related genes	Relation type
ENSG00000267459	TF binding region
ENSG00000267776	TF binding region
SLC25A36P1	TF binding region
ENSG00000267781	Chromatin interaction
ENSG00000018869	Chromatin interaction
ENSG00000267454	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10405914	0.83[CHB][hapmap]
rs10418348	0.82[CHB][hapmap]
rs10419074	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs10419213	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs12608563	0.86[ASN][1000 genomes]
rs12610246	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12610899	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12978696	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12981331	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12983342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2288856	0.89[CHB][hapmap];0.92[CHD][hapmap]
rs2304123	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2304125	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2304126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2304127	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4801717	0.88[CHB][hapmap]
rs8111942	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1017102	ZNF134	cis	cerebellum	SCAN
rs1017102	ZNF324	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56881200-56904000	ZNF genes & repeats	Liver	Liver
2	chr19:56881400-56893000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:56888800-56892800	Weak transcription	Colonic Mucosa	Colon
4	chr19:56889200-56897400	Weak transcription	Gastric	stomach
5	chr19:56889200-56901200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:56889200-56904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:56889400-56895200	Weak transcription	Brain Angular Gyrus	brain
8	chr19:56889400-56895400	Weak transcription	Brain Substantia Nigra	brain
9	chr19:56889400-56895600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:56889400-56904000	Weak transcription	Fetal Heart	heart
11	chr19:56889400-56904000	Weak transcription	K562	blood
12	chr19:56890000-56894400	Weak transcription	Brain Anterior Caudate	brain
13	chr19:56890000-56900200	Weak transcription	Right Ventricle	heart
14	chr19:56890200-56894200	Weak transcription	Brain Germinal Matrix	brain
15	chr19:56890200-56895200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:56890200-56895400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr19:56890200-56903600	Weak transcription	Fetal Brain Male	brain
18	chr19:56890400-56894400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:56890600-56893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:56890600-56894000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:56890600-56894600	Weak transcription	Fetal Kidney	kidney
22	chr19:56890600-56895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:56890600-56900200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:56890600-56900400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:56890600-56904000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:56890800-56894200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr19:56890800-56894400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:56890800-56895200	Weak transcription	Psoas Muscle	Psoas
29	chr19:56890800-56895600	Weak transcription	Left Ventricle	heart
30	chr19:56891200-56895000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:56891200-56895400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr19:56891600-56893200	ZNF genes & repeats	Adipose Nuclei	Adipose
33	chr19:56891600-56893200	ZNF genes & repeats	Aorta	Aorta
34	chr19:56892000-56894400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:56892000-56894800	Weak transcription	Brain Hippocampus Middle	brain
36	chr19:56892000-56894800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr19:56892400-56894200	Weak transcription	Fetal Brain Female	brain
38	chr19:56892400-56894400	Weak transcription	Fetal Lung	lung

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