Variant report

Variant	rs4741508
Chromosome Location	chr9:15469733-15469734
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:15465896..15468103-chr9:15469052..15471427,2	K562	blood:
2	chr9:15466603..15468286-chr9:15468644..15471427,2	K562	blood:
3	chr9:15460438..15462914-chr9:15467328..15469967,2	K562	blood:
4	chr9:15469088..15470656-chr9:15499261..15501124,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10081655	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10115540	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10117968	0.87[CHB][hapmap];0.92[MKK][hapmap]
rs1033056	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1046388	0.88[AFR][1000 genomes]
rs10733292	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10738392	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10738393	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10738395	0.84[ASW][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap]
rs10738397	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10738398	0.91[AFR][1000 genomes]
rs10756664	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10756666	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10962036	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1123038	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs12093	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs12339417	0.90[LWK][hapmap]
rs1397214	0.87[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap]
rs1397215	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1976599	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2175259	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs2382530	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2665504	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs2737829	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2737842	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2777950	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]
rs4741500	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs4741501	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4741502	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4741504	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4741505	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4741506	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4741507	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6474915	0.81[CHB][hapmap];0.89[YRI][hapmap]
rs6474916	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes]
rs6474918	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs6474923	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7018658	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7021042	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7026910	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7026970	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7037580	0.80[AFR][1000 genomes]
rs7042165	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7046713	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7862428	0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs907075	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs907076	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9650682	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs9650683	1.00[CHB][hapmap];0.94[JPT][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4741508	C9orf150	cis	cerebellum	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	chr9:15438400-15469800	Strong transcription	Primary B cells from peripheral blood	blood
3	chr9:15439000-15492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:15442600-15478200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr9:15442600-15478600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:15442800-15508400	Strong transcription	Fetal Thymus	thymus
7	chr9:15443000-15470200	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr9:15443000-15478000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr9:15443000-15482200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:15443200-15478000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr9:15443200-15479600	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr9:15443200-15490400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:15443200-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:15443400-15479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr9:15443600-15470400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:15443800-15492200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr9:15444000-15482000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:15444000-15487600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:15444000-15492400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:15444400-15495200	Weak transcription	Fetal Heart	heart
21	chr9:15444600-15491200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:15444800-15482200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:15447000-15509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:15447400-15469800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:15448200-15472200	Weak transcription	Aorta	Aorta
26	chr9:15448200-15482200	Weak transcription	Psoas Muscle	Psoas
27	chr9:15448400-15480000	Weak transcription	Stomach Mucosa	stomach
28	chr9:15448600-15476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:15449000-15492200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:15449800-15478000	Strong transcription	Fetal Lung	lung
31	chr9:15449800-15509000	Weak transcription	Small Intestine	intestine
32	chr9:15452200-15480200	Weak transcription	Brain Substantia Nigra	brain
33	chr9:15452200-15492400	Weak transcription	Right Ventricle	heart
34	chr9:15452600-15470000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:15454200-15478600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:15454600-15508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:15456200-15470200	Strong transcription	Adipose Nuclei	Adipose
38	chr9:15456200-15480600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:15456400-15471600	Strong transcription	HUVEC	blood vessel
40	chr9:15457000-15482000	Strong transcription	Dnd41	blood
41	chr9:15457000-15492400	Weak transcription	Lung	lung
42	chr9:15457200-15470000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:15457400-15471400	Strong transcription	Placenta	Placenta
44	chr9:15458200-15475600	Strong transcription	GM12878-XiMat	blood
45	chr9:15458200-15478200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr9:15458800-15470600	Strong transcription	Primary T cells from cord blood	blood
47	chr9:15459000-15492200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr9:15459600-15469800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:15460000-15476000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr9:15460800-15510000	Weak transcription	Esophagus	oesophagus

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