Variant report

Variant	rs17428858
Chromosome Location	chr12:117133400-117133401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117129402..117130962-chr12:117132498..117134381,2	K562	blood:
2	chr12:117124906..117127466-chr12:117130857..117133400,3	MCF-7	breast:
3	chr12:117126789..117129460-chr12:117131891..117135888,3	MCF-7	breast:
4	chr12:117124747..117126838-chr12:117131104..117134060,2	K562	blood:

Extended variants
information (count: 3 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7974008	0.82[EUR][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	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv521649	chr12:117127540-117136787	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17428858	TESC	cis	parietal	SCAN
rs17428858	ATXN2	cis	cerebellum	SCAN
rs17428858	SDS	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117127600-117134800	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr12:117131800-117134000	Enhancers	Primary hematopoietic stem cells	blood
3	chr12:117131800-117134200	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr12:117131800-117134600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr12:117131800-117135400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:117132000-117133800	Weak transcription	Gastric	stomach
7	chr12:117132000-117134200	Bivalent Enhancer	Primary B cells from cord blood	blood
8	chr12:117132000-117134400	Weak transcription	Pancreas	Pancrea
9	chr12:117132000-117141200	Weak transcription	Lung	lung
10	chr12:117132200-117133400	Enhancers	Fetal Brain Female	brain
11	chr12:117132200-117134800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:117132200-117147000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:117132400-117133400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:117132400-117133400	Enhancers	Brain Germinal Matrix	brain
15	chr12:117132400-117147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:117133000-117133400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:117133000-117133400	Enhancers	Thymus	Thymus
18	chr12:117133000-117133400	Enhancers	Spleen	Spleen
19	chr12:117133000-117133400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
20	chr12:117133000-117133800	Weak transcription	Liver	Liver
21	chr12:117133000-117135600	Enhancers	A549	lung
22	chr12:117133000-117136200	Enhancers	Fetal Thymus	thymus
23	chr12:117133200-117134000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:117133200-117135200	Weak transcription	Left Ventricle	heart
25	chr12:117133200-117135200	Weak transcription	Right Atrium	heart
26	chr12:117133200-117135200	Weak transcription	Right Ventricle	heart
27	chr12:117133400-117134200	Weak transcription	Spleen	Spleen
28	chr12:117133400-117135200	Weak transcription	Brain Germinal Matrix	brain
29	chr12:117133400-117135200	Weak transcription	Fetal Brain Female	brain

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