Variant report

Variant	rs3802656
Chromosome Location	chr10:90975649-90975650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11594137	0.82[CHD][hapmap]
rs12246667	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12780342	1.00[JPT][hapmap]
rs2254636	1.00[JPT][hapmap]
rs4933497	0.84[CHD][hapmap]
rs7908760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758235	chr10:90835064-91017486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2759775	chr10:90835064-91017486	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1038123	chr10:90954417-90992129	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1040280	chr10:90962032-90979093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1042428	chr10:90962252-90977164	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3802656	LIPA	cis	cerebellum	SCAN
rs3802656	PAPSS2	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90967600-90987200	Weak transcription	Aorta	Aorta
2	chr10:90968200-90977000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr10:90968200-90977000	Weak transcription	HSMM	muscle
4	chr10:90968200-90979800	Weak transcription	Ovary	ovary
5	chr10:90968200-90983400	Weak transcription	NHLF	lung
6	chr10:90968200-90994800	Weak transcription	Gastric	stomach
7	chr10:90968400-90979400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr10:90968400-90979400	Weak transcription	Esophagus	oesophagus
9	chr10:90968400-90979400	Weak transcription	Lung	lung
10	chr10:90968400-90979600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr10:90968400-90987200	Weak transcription	Pancreas	Pancrea
12	chr10:90968400-91000800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:90968400-91002200	Weak transcription	Right Ventricle	heart
14	chr10:90968600-90977000	Weak transcription	HUVEC	blood vessel
15	chr10:90969000-90977000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:90969600-90977000	Weak transcription	Fetal Thymus	thymus
17	chr10:90970800-90984600	Weak transcription	Fetal Brain Female	brain
18	chr10:90971000-90977200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr10:90971400-90977000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr10:90971400-90977000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:90971400-90980600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr10:90971400-90984600	Weak transcription	Fetal Brain Male	brain
23	chr10:90971600-90977000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr10:90971600-90977000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr10:90971800-90977000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:90972000-90977000	Weak transcription	Hela-S3	cervix
27	chr10:90972200-90977000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr10:90972800-90977000	Weak transcription	HSMMtube	muscle
29	chr10:90973000-90979400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr10:90973200-90975800	Genic enhancers	Brain Anterior Caudate	brain
31	chr10:90973200-90977000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr10:90973200-90977600	Enhancers	Brain Angular Gyrus	brain
33	chr10:90973400-90975800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr10:90973400-90976000	Strong transcription	Primary hematopoietic stem cells	blood
35	chr10:90973400-90976000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:90973400-90976000	Strong transcription	Placenta	Placenta
37	chr10:90973400-90976000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr10:90973400-90977000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr10:90973400-90977000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr10:90973400-90977000	Weak transcription	Fetal Lung	lung
41	chr10:90973400-90977000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr10:90973400-90977000	Weak transcription	Stomach Mucosa	stomach
43	chr10:90973600-90975800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr10:90973600-90975800	Strong transcription	Adipose Nuclei	Adipose
45	chr10:90973600-90975800	Strong transcription	Liver	Liver
46	chr10:90973600-90976000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr10:90973600-90976000	Strong transcription	Primary B cells from cord blood	blood
48	chr10:90973600-90976000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr10:90973600-90976000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr10:90973600-90977000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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