Variant report

Variant	rs16924626
Chromosome Location	chr9:6480726-6480727
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6478983..6480805-chr9:6480868..6482878,2	K562	blood:

Variant related genes	Relation type
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10115883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10122116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10124572	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10125914	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739098	0.94[JPT][hapmap]
rs10739099	0.95[JPT][hapmap]
rs10758784	0.89[JPT][hapmap]
rs10758785	0.89[JPT][hapmap]
rs10758788	0.90[JPT][hapmap]
rs10758789	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10758790	0.89[JPT][hapmap]
rs10815428	0.95[JPT][hapmap]
rs10975583	0.94[JPT][hapmap]
rs10975585	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10975595	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs10975603	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10975605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1156747	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11790625	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11791651	0.93[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11795355	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12346455	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs12347573	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12351293	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13283381	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs13289925	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13291472	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13292799	0.81[ASN][1000 genomes]
rs13296970	0.80[EUR][1000 genomes]
rs13298500	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs13301146	0.80[EUR][1000 genomes]
rs13440427	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1381035	0.89[JPT][hapmap]
rs16924328	0.86[JPT][hapmap]
rs16924562	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16924591	0.85[ASN][1000 genomes]
rs16924624	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16924631	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16924634	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1870696	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1903419	0.88[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs2169283	0.81[CHB][hapmap]
rs2169286	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2282158	0.88[CHB][hapmap]
rs2297443	0.83[CHB][hapmap]
rs33962342	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs3739654	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3818705	0.94[CHB][hapmap]
rs4380997	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4384035	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4463484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4556138	0.87[ASN][1000 genomes]
rs4740844	0.90[JPT][hapmap]
rs4742201	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs4742202	0.89[JPT][hapmap]
rs504698	0.85[ASN][1000 genomes]
rs530722	0.83[ASN][1000 genomes]
rs55960819	0.83[ASN][1000 genomes]
rs56396114	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56939673	0.85[EUR][1000 genomes]
rs569866	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6477086	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6477087	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66509816	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7027302	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7029772	0.94[CHB][hapmap]
rs7034328	0.96[ASN][1000 genomes]
rs73399080	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73401025	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7847675	0.86[ASN][1000 genomes]
rs7852539	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7857628	1.00[JPT][hapmap]
rs7865955	1.00[JPT][hapmap]
rs7873756	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7876000	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	esv2535857	chr9:6479763-6481183	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv892162	chr9:6480005-6788085	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16924626	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6435400-6482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:6450000-6482800	Weak transcription	Pancreas	Pancrea
3	chr9:6452600-6488000	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:6452800-6481600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:6452800-6485400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr9:6452800-6485400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:6458600-6482800	Weak transcription	Gastric	stomach
8	chr9:6458800-6497200	Weak transcription	Colonic Mucosa	Colon
9	chr9:6459400-6501800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:6460600-6486800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:6461400-6486000	Weak transcription	K562	blood
12	chr9:6463600-6518400	Weak transcription	Fetal Brain Male	brain
13	chr9:6467400-6486200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:6467400-6497200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:6468600-6481600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:6468800-6482000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:6468800-6482000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:6468800-6482200	Weak transcription	Brain Anterior Caudate	brain
19	chr9:6470000-6481800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr9:6471600-6482800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:6471600-6501800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:6471600-6504600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:6472200-6497200	Weak transcription	Aorta	Aorta
24	chr9:6472200-6508200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:6473000-6491600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:6473000-6499600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr9:6473800-6498400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:6473800-6506200	Weak transcription	Small Intestine	intestine
29	chr9:6474400-6490600	Strong transcription	HUVEC	blood vessel
30	chr9:6474800-6502800	Strong transcription	Dnd41	blood
31	chr9:6475000-6488400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:6475200-6503000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr9:6475400-6482400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:6475400-6490400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr9:6475400-6491800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr9:6475400-6491800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr9:6475400-6494400	Strong transcription	Fetal Thymus	thymus
38	chr9:6475400-6508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr9:6475400-6508400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:6475400-6508800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr9:6475400-6508800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr9:6475600-6494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:6475800-6483200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr9:6475800-6484600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr9:6475800-6488200	Strong transcription	Adipose Nuclei	Adipose
46	chr9:6475800-6491000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr9:6475800-6491800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:6475800-6492000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:6475800-6492800	Strong transcription	GM12878-XiMat	blood
50	chr9:6475800-6493000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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