Variant report

Variant	rs12935890
Chromosome Location	chr17:46090769-46090770
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45973275..45976103-chr17:46088600..46091071,2	K562	blood:
2	chr17:46058200..46059806-chr17:46090614..46093225,2	MCF-7	breast:
3	chr17:46050479..46052242-chr17:46089337..46091891,2	K562	blood:
4	chr17:46089884..46092487-chr17:46093385..46095958,2	MCF-7	breast:
5	chr17:46087197..46088712-chr17:46089794..46092489,2	MCF-7	breast:
6	chr17:46083701..46085989-chr17:46089198..46091342,3	K562	blood:

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2525103	0.94[EUR][1000 genomes]
rs33983467	0.81[AMR][1000 genomes]
rs34785219	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35662223	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12935890	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46089400-46095000	Weak transcription	A549	lung
2	chr17:46089600-46092800	Enhancers	Fetal Brain Male	brain
3	chr17:46089800-46091000	Enhancers	Brain Cingulate Gyrus	brain
4	chr17:46089800-46091200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:46089800-46091200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr17:46089800-46091400	Enhancers	Fetal Thymus	thymus
7	chr17:46089800-46092400	Enhancers	Brain Hippocampus Middle	brain
8	chr17:46089800-46092800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr17:46089800-46094000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr17:46090000-46091000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:46090000-46092400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
12	chr17:46090000-46092600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:46090000-46093400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:46090000-46093600	Weak transcription	HSMM	muscle
15	chr17:46090000-46095800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:46090200-46091000	Enhancers	Brain Angular Gyrus	brain
17	chr17:46090200-46091200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
18	chr17:46090200-46091200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
19	chr17:46090200-46092200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr17:46090200-46092800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
21	chr17:46090200-46092800	Enhancers	Brain Germinal Matrix	brain
22	chr17:46090200-46093600	Weak transcription	Spleen	Spleen
23	chr17:46090200-46093800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr17:46090200-46100400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr17:46090200-46100400	Weak transcription	Brain Substantia Nigra	brain
26	chr17:46090400-46091200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
27	chr17:46090400-46091600	Weak transcription	Placenta	Placenta
28	chr17:46090400-46091600	Weak transcription	K562	blood
29	chr17:46090400-46091800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:46090400-46092000	Weak transcription	Brain Anterior Caudate	brain
31	chr17:46090400-46092200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
32	chr17:46090400-46092800	Enhancers	Fetal Brain Female	brain
33	chr17:46090400-46093400	Weak transcription	HSMMtube	muscle
34	chr17:46090400-46100800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr17:46090600-46090800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
36	chr17:46090600-46091000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:46090600-46091400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:46090600-46091600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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