Variant report

Variant	rs2777950
Chromosome Location	chr9:15472139-15472140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10283923	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10283927	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1046388	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10738393	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10738395	0.84[ASW][hapmap];0.96[YRI][hapmap]
rs10738397	1.00[ASW][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10738398	0.86[AFR][1000 genomes]
rs10756666	1.00[ASW][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs10962036	0.86[AFR][1000 genomes]
rs10962048	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs12336503	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12336509	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12339417	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12380487	0.82[CHB][hapmap]
rs12683553	0.94[ASN][1000 genomes]
rs12686545	0.91[ASN][1000 genomes]
rs13288118	1.00[CHB][hapmap]
rs13289935	1.00[CHB][hapmap]
rs1397214	0.85[YRI][hapmap]
rs16933311	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs16933316	1.00[CHB][hapmap]
rs16933320	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs16933348	0.89[ASN][1000 genomes]
rs1828383	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2175257	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277191	0.87[ASN][1000 genomes]
rs2382530	0.88[AFR][1000 genomes]
rs2777949	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs28515581	0.82[AMR][1000 genomes]
rs28537229	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4741501	0.83[AFR][1000 genomes]
rs4741502	0.90[AFR][1000 genomes]
rs4741505	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4741507	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4741508	1.00[ASW][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs55771541	0.85[ASN][1000 genomes]
rs56361298	0.89[ASN][1000 genomes]
rs57467578	0.89[ASN][1000 genomes]
rs58607272	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59639757	0.85[ASN][1000 genomes]
rs62571010	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62571022	0.89[ASN][1000 genomes]
rs62571023	0.89[ASN][1000 genomes]
rs62571024	0.89[ASN][1000 genomes]
rs62571027	0.84[ASN][1000 genomes]
rs62571030	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6474915	0.89[YRI][hapmap]
rs6474916	0.89[YRI][hapmap]
rs6474927	0.82[ASN][1000 genomes]
rs7018658	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7021042	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7021153	0.84[ASN][1000 genomes]
rs7026910	0.88[AFR][1000 genomes]
rs73408328	0.89[ASN][1000 genomes]
rs7856318	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs7857933	0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs7862428	0.84[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7863046	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7863139	0.98[ASN][1000 genomes]
rs907075	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs907076	1.00[ASW][hapmap];0.90[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs9650682	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2777950	C9orf150	cis	cerebellum	SCAN
rs2777950	C9orf93	cis	cerebellum	SCAN
rs2777950	ADAMTSL1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15433400-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:15439000-15492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:15442600-15478200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr9:15442600-15478600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:15442800-15508400	Strong transcription	Fetal Thymus	thymus
6	chr9:15443000-15478000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:15443000-15482200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:15443200-15478000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr9:15443200-15479600	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr9:15443200-15490400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:15443200-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:15443400-15479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:15443800-15492200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:15444000-15482000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:15444000-15487600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:15444000-15492400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:15444400-15495200	Weak transcription	Fetal Heart	heart
18	chr9:15444600-15491200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:15444800-15482200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:15447000-15509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:15448200-15472200	Weak transcription	Aorta	Aorta
22	chr9:15448200-15482200	Weak transcription	Psoas Muscle	Psoas
23	chr9:15448400-15480000	Weak transcription	Stomach Mucosa	stomach
24	chr9:15448600-15476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:15449000-15492200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:15449800-15478000	Strong transcription	Fetal Lung	lung
27	chr9:15449800-15509000	Weak transcription	Small Intestine	intestine
28	chr9:15452200-15480200	Weak transcription	Brain Substantia Nigra	brain
29	chr9:15452200-15492400	Weak transcription	Right Ventricle	heart
30	chr9:15454200-15478600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:15454600-15508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:15456200-15480600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:15457000-15482000	Strong transcription	Dnd41	blood
34	chr9:15457000-15492400	Weak transcription	Lung	lung
35	chr9:15458200-15475600	Strong transcription	GM12878-XiMat	blood
36	chr9:15458200-15478200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr9:15459000-15492200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr9:15460000-15476000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:15460800-15510000	Weak transcription	Esophagus	oesophagus
40	chr9:15461000-15492200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr9:15461400-15478000	Strong transcription	Primary B cells from cord blood	blood
42	chr9:15461600-15483800	Weak transcription	Fetal Intestine Small	intestine
43	chr9:15461600-15492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:15461600-15492800	Weak transcription	Pancreas	Pancrea
45	chr9:15462200-15482200	Weak transcription	Brain Angular Gyrus	brain
46	chr9:15462400-15478600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr9:15462800-15505200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:15463000-15476400	Weak transcription	NHEK	skin
49	chr9:15463800-15478600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr9:15465000-15473200	Strong transcription	Rectal Mucosa Donor 31	rectum

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