Variant report

Variant	rs17389665
Chromosome Location	chr10:98208881-98208882
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11599620	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs2025453	0.83[CHD][hapmap]
rs3789955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919022	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61857573	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61857628	0.84[EUR][1000 genomes]
rs7067562	1.00[YRI][hapmap]
rs7070439	0.83[CHD][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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv831950	chr10:98080972-98245434	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17389665	HPS1	cis	cerebellum	SCAN
rs17389665	NKX2-3	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98206400-98209400	Enhancers	Fetal Heart	heart
2	chr10:98206600-98209200	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr10:98206600-98211200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr10:98206600-98212600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:98207000-98210200	Weak transcription	Fetal Brain Female	brain
6	chr10:98207400-98209200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr10:98207400-98209400	Enhancers	GM12878-XiMat	blood
8	chr10:98208000-98209000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr10:98208000-98209000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:98208000-98209600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:98208000-98209800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr10:98208200-98209000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr10:98208200-98209200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:98208200-98209200	Weak transcription	Right Ventricle	heart
15	chr10:98208200-98209800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:98208400-98209000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr10:98208400-98209400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr10:98208400-98209800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr10:98208400-98209800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:98208600-98209000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr10:98208600-98209800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr10:98208800-98209800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr10:98208800-98210800	Enhancers	H1 Cell Line	embryonic stem cell

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