Variant report

Variant	rs882163
Chromosome Location	chr17:46093539-46093540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46091408..46093930-chr17:46096491..46098890,2	MCF-7	breast:
2	chr17:46019148..46022019-chr17:46092699..46095180,2	K562	blood:
3	chr17:46025314..46027169-chr17:46093324..46095871,2	K562	blood:
4	chr17:45973797..45976110-chr17:46092219..46094181,2	MCF-7	breast:
5	chr17:46042235..46044126-chr17:46090847..46093838,2	K562	blood:
6	chr17:46089884..46092487-chr17:46093385..46095958,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264019	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6503985	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs757351	0.84[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs882163	C17orf46	cis	parietal	SCAN
rs882163	PNPO	cis	parietal	SCAN
rs882163	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs882163	PNPO	cis	cerebellum	SCAN
rs882163	HOXB6	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46089400-46095000	Weak transcription	A549	lung
2	chr17:46089800-46094000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr17:46090000-46093600	Weak transcription	HSMM	muscle
4	chr17:46090000-46095800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr17:46090200-46093600	Weak transcription	Spleen	Spleen
6	chr17:46090200-46093800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:46090200-46100400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:46090200-46100400	Weak transcription	Brain Substantia Nigra	brain
9	chr17:46090400-46100800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr17:46091400-46095000	Weak transcription	Fetal Thymus	thymus
11	chr17:46091400-46095800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr17:46091600-46094000	Enhancers	Fetal Stomach	stomach
13	chr17:46092200-46095200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:46092600-46093800	Weak transcription	Brain Anterior Caudate	brain
15	chr17:46092600-46094400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:46092600-46094400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:46092600-46100400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr17:46092600-46100800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:46092600-46100800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr17:46092800-46093800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:46092800-46093800	Weak transcription	Fetal Brain Male	brain
22	chr17:46092800-46095000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:46092800-46100200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr17:46092800-46100400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr17:46092800-46100600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:46092800-46100600	Weak transcription	Fetal Brain Female	brain
27	chr17:46093000-46093800	Weak transcription	Placenta	Placenta
28	chr17:46093200-46093600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr17:46093400-46093800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:46093400-46094000	Enhancers	HSMMtube	muscle
31	chr17:46093400-46094000	Enhancers	K562	blood

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