Variant report

Variant	rs10491838
Chromosome Location	chr9:6438023-6438024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10115294	0.96[EUR][1000 genomes]
rs10123605	0.96[EUR][1000 genomes]
rs10125313	0.96[EUR][1000 genomes]
rs1037885	0.91[EUR][1000 genomes]
rs1048279	0.88[EUR][1000 genomes]
rs10739096	0.96[EUR][1000 genomes]
rs10739101	1.00[EUR][1000 genomes]
rs10739103	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10739104	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10758762	0.91[EUR][1000 genomes]
rs10758763	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10758768	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815400	0.96[EUR][1000 genomes]
rs10815401	0.96[EUR][1000 genomes]
rs10815429	0.87[EUR][1000 genomes]
rs10815430	0.96[EUR][1000 genomes]
rs1156869	1.00[EUR][1000 genomes]
rs12346381	0.88[EUR][1000 genomes]
rs1322170	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13283464	0.83[EUR][1000 genomes]
rs13283631	0.83[EUR][1000 genomes]
rs13283687	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13284392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13285125	0.83[EUR][1000 genomes]
rs13285152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13285458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13288875	0.83[EUR][1000 genomes]
rs13290488	0.83[EUR][1000 genomes]
rs13291494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13291887	0.83[EUR][1000 genomes]
rs13293015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13293673	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13294924	0.83[EUR][1000 genomes]
rs13296481	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13296692	0.83[EUR][1000 genomes]
rs13298872	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13299896	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13300059	0.83[EUR][1000 genomes]
rs13302032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1330381	0.96[EUR][1000 genomes]
rs1381038	0.91[EUR][1000 genomes]
rs1407357	0.91[EUR][1000 genomes]
rs1407358	0.91[EUR][1000 genomes]
rs1412420	0.88[EUR][1000 genomes]
rs1854709	0.88[EUR][1000 genomes]
rs1855022	0.84[EUR][1000 genomes]
rs2000198	0.88[EUR][1000 genomes]
rs2019737	0.91[EUR][1000 genomes]
rs2051003	0.88[EUR][1000 genomes]
rs2150964	0.81[EUR][1000 genomes]
rs2150971	0.88[EUR][1000 genomes]
rs2381438	0.84[EUR][1000 genomes]
rs28615746	0.96[EUR][1000 genomes]
rs2890707	0.91[EUR][1000 genomes]
rs34530211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34581400	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35301257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35408061	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36089474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3847262	0.91[EUR][1000 genomes]
rs3858051	0.91[EUR][1000 genomes]
rs4008347	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs424119	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4475552	0.84[EUR][1000 genomes]
rs4742172	0.96[EUR][1000 genomes]
rs4742177	0.91[EUR][1000 genomes]
rs4742180	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742198	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4742200	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4742203	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs503315	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs553048	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6477060	0.88[EUR][1000 genomes]
rs6477067	0.91[EUR][1000 genomes]
rs67541153	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67797327	0.83[EUR][1000 genomes]
rs7021445	0.96[EUR][1000 genomes]
rs7031407	0.96[EUR][1000 genomes]
rs7031967	0.92[EUR][1000 genomes]
rs7032411	0.86[AMR][1000 genomes]
rs7035574	0.88[EUR][1000 genomes]
rs7036990	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7039968	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7040374	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7043824	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7043887	0.96[EUR][1000 genomes]
rs7044749	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7048431	0.84[EUR][1000 genomes]
rs72693587	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7350177	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7851921	0.96[EUR][1000 genomes]
rs7852138	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853322	0.92[EUR][1000 genomes]
rs7858373	0.91[EUR][1000 genomes]
rs7859139	0.91[EUR][1000 genomes]
rs7864212	0.91[EUR][1000 genomes]
rs7869419	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7873206	0.96[EUR][1000 genomes]
rs898673	0.91[EUR][1000 genomes]
rs922221	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980849	0.96[EUR][1000 genomes]
rs980850	0.88[EUR][1000 genomes]
rs993952	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10491838	C9orf38	Cis_1M	lymphoblastoid	RTeQTL
rs10491838	UHRF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6439400	Weak transcription	Colonic Mucosa	Colon
2	chr9:6414600-6449000	Weak transcription	Gastric	stomach
3	chr9:6414600-6449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
5	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
6	chr9:6415600-6441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
8	chr9:6415800-6442800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:6416000-6438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:6417800-6440000	Weak transcription	Fetal Brain Female	brain
12	chr9:6418000-6438200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:6421400-6449400	Weak transcription	Liver	Liver
14	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
15	chr9:6422800-6446400	Weak transcription	Brain Germinal Matrix	brain
16	chr9:6422800-6449200	Weak transcription	Pancreas	Pancrea
17	chr9:6423400-6440800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:6426200-6439800	Weak transcription	NHLF	lung
19	chr9:6428200-6443200	Weak transcription	Fetal Kidney	kidney
20	chr9:6429200-6462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:6429600-6449200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr9:6431200-6449000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr9:6431200-6449200	Weak transcription	Adipose Nuclei	Adipose
24	chr9:6431400-6438400	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:6431600-6438200	Weak transcription	Colon Smooth Muscle	Colon
26	chr9:6431600-6440000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:6431600-6441000	Weak transcription	Left Ventricle	heart
28	chr9:6431600-6442000	Weak transcription	Right Atrium	heart
29	chr9:6431600-6444200	Weak transcription	HSMMtube	muscle
30	chr9:6431600-6444400	Weak transcription	Right Ventricle	heart
31	chr9:6432000-6438200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:6432000-6443000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:6433000-6443000	Strong transcription	Fetal Thymus	thymus
34	chr9:6433000-6444200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr9:6433200-6439200	Weak transcription	Psoas Muscle	Psoas
36	chr9:6433400-6441400	Strong transcription	Dnd41	blood
37	chr9:6433600-6438600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:6433600-6438600	Weak transcription	Stomach Mucosa	stomach
39	chr9:6433800-6438600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:6433800-6438800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr9:6433800-6439600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:6434000-6438800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr9:6434200-6438600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:6434200-6439400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:6434400-6438600	Strong transcription	Primary B cells from cord blood	blood
46	chr9:6434400-6449200	Weak transcription	A549	lung
47	chr9:6434600-6438400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr9:6434600-6441400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:6434800-6447200	Weak transcription	Brain Anterior Caudate	brain
50	chr9:6435000-6439200	Strong transcription	Primary B cells from peripheral blood	blood

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