Variant report

Variant	rs3789955
Chromosome Location	chr10:98205419-98205420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11591933	1.00[ASW][hapmap]
rs11594403	1.00[ASW][hapmap]
rs11599620	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs17389665	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]
rs17391197	1.00[ASW][hapmap]
rs17392013	1.00[ASW][hapmap]
rs2025453	0.83[CHD][hapmap]
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]
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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3789955	HPS1	cis	cerebellum	SCAN
rs3789955	NKX2-3	cis	cerebellum	SCAN
rs3789955	TCTN3	cis	brain	BrainEAC
rs3789955	PRSS21	trans	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98201000-98205800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:98201800-98206800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:98202000-98208000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr10:98202200-98206600	Weak transcription	Left Ventricle	heart
5	chr10:98202400-98206400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr10:98202400-98206400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr10:98202400-98206400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr10:98202400-98206600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:98202400-98206800	Weak transcription	Right Ventricle	heart
10	chr10:98202400-98207000	Weak transcription	Spleen	Spleen
11	chr10:98202400-98207600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr10:98202600-98206200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr10:98202600-98206600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr10:98202600-98206600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:98202600-98206600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:98202600-98206800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr10:98202600-98207200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:98203000-98206200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:98205000-98208200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:98205000-98208600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:98205400-98205600	Active TSS	Gastric	stomach
22	chr10:98205400-98206000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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