Variant report

Variant	rs3112998
Chromosome Location	chr2:95822447-95822448
allele	A/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	JUND	chr2:95822353-95822657	HepG2	liver:	n/a	chr2:95822504-95822515

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95787747..95790695-chr2:95821502..95823439,2	K562	blood:
2	chr2:95820602..95822831-chr2:95829587..95831468,2	MCF-7	breast:

Variant related genes	Relation type
ZNF514	TF binding region
ENSG00000163067	Chromatin interaction
ENSG00000144026	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2113418	0.93[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap]
rs3112226	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3112989	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3112992	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3112994	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6719142	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs889854	0.89[ASW][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3112998	ZNF514	cis	cerebellum	SCAN
rs3112998	ZNF514	cis	multi-tissue	Pritchard
rs3112998	ACTR1B	cis	cerebellum	SCAN
rs3112998	ZNF514	Cis_1M	lymphoblastoid	RTeQTL
rs3112998	SRA1	trans	parietal	SCAN
rs3112998	ZNF514	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95803600-95822600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
2	chr2:95807800-95823200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:95808000-95823200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:95808200-95823000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
5	chr2:95808200-95823400	ZNF genes & repeats	Liver	Liver
6	chr2:95808400-95823800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:95809400-95823000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:95809400-95824600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:95809600-95823600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:95809600-95823600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:95809600-95823800	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr2:95809800-95823600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:95810000-95822800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
14	chr2:95810000-95824400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:95811400-95823400	ZNF genes & repeats	Fetal Stomach	stomach
16	chr2:95811400-95823800	ZNF genes & repeats	NHDF-Ad	bronchial
17	chr2:95812200-95824400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:95812200-95824400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr2:95812400-95822800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr2:95812400-95824600	ZNF genes & repeats	A549	lung
21	chr2:95813800-95822800	ZNF genes & repeats	Aorta	Aorta
22	chr2:95813800-95822800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
23	chr2:95814000-95823400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:95814000-95824400	ZNF genes & repeats	HSMMtube	muscle
25	chr2:95814200-95823000	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr2:95814400-95823800	ZNF genes & repeats	NHLF	lung
27	chr2:95814800-95822800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
28	chr2:95815000-95822800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr2:95815400-95823000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:95818200-95822800	Strong transcription	Fetal Kidney	kidney
31	chr2:95818200-95823200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr2:95818600-95824000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:95818600-95824600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:95818800-95823600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:95819000-95822800	Strong transcription	Placenta	Placenta
36	chr2:95819000-95823000	Strong transcription	Brain Angular Gyrus	brain
37	chr2:95819000-95824000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:95819000-95824200	Weak transcription	HUVEC	blood vessel
39	chr2:95819000-95824400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:95819200-95823000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:95819200-95823400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:95819400-95823800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:95819600-95824200	Weak transcription	Fetal Thymus	thymus
44	chr2:95819800-95823000	ZNF genes & repeats	Esophagus	oesophagus
45	chr2:95820000-95822600	Strong transcription	Psoas Muscle	Psoas
46	chr2:95820000-95824400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:95820200-95822800	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr2:95820200-95822800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:95820200-95823000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:95820200-95823000	Strong transcription	Brain Hippocampus Middle	brain

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