Variant report

Variant	rs10815435
Chromosome Location	chr9:6437518-6437519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10124572	0.86[ASN][1000 genomes]
rs10733529	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10739098	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739099	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739100	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739102	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10758784	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10758785	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10758786	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10758787	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10758788	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10758789	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10758790	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10758791	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10758792	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10975579	0.82[ASN][1000 genomes]
rs10975582	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10975583	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10975585	0.86[ASN][1000 genomes]
rs10975595	0.91[ASN][1000 genomes]
rs1156747	0.87[ASN][1000 genomes]
rs11790625	0.88[ASN][1000 genomes]
rs11791651	0.82[ASN][1000 genomes]
rs12346455	0.82[ASN][1000 genomes]
rs12351293	0.86[ASN][1000 genomes]
rs13292799	0.89[ASN][1000 genomes]
rs13440427	0.87[ASN][1000 genomes]
rs1381035	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1381036	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1381037	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16924562	0.90[ASN][1000 genomes]
rs16924591	0.83[ASN][1000 genomes]
rs1824537	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1870696	0.88[ASN][1000 genomes]
rs1903419	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2065074	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2065075	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2169283	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2169286	0.86[ASN][1000 genomes]
rs2381444	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3739654	0.82[ASN][1000 genomes]
rs380674	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs394137	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs414107	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4384035	0.85[ASN][1000 genomes]
rs452135	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4556138	0.81[ASN][1000 genomes]
rs4740844	0.88[ASN][1000 genomes]
rs4740845	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4742199	0.88[ASN][1000 genomes]
rs4742201	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742202	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742204	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs504698	0.83[ASN][1000 genomes]
rs530722	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs55960819	0.86[ASN][1000 genomes]
rs56218473	0.88[ASN][1000 genomes]
rs56396114	0.86[ASN][1000 genomes]
rs56939673	0.83[ASN][1000 genomes]
rs569866	0.83[ASN][1000 genomes]
rs7027302	0.86[ASN][1000 genomes]
rs7033570	0.87[ASN][1000 genomes]
rs7033940	0.97[ASN][1000 genomes]
rs73401679	0.97[ASN][1000 genomes]
rs7853059	0.97[ASN][1000 genomes]
rs7853834	0.97[ASN][1000 genomes]
rs7860966	0.90[ASN][1000 genomes]
rs7861073	0.90[ASN][1000 genomes]
rs7861559	0.90[ASN][1000 genomes]
rs7871134	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10815435	C9orf38	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	chr9:6417600-6437800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:6417800-6440000	Weak transcription	Fetal Brain Female	brain
13	chr9:6418000-6438200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:6419200-6437800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr9:6421400-6449400	Weak transcription	Liver	Liver
16	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
17	chr9:6422800-6446400	Weak transcription	Brain Germinal Matrix	brain
18	chr9:6422800-6449200	Weak transcription	Pancreas	Pancrea
19	chr9:6423400-6440800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:6426200-6439800	Weak transcription	NHLF	lung
21	chr9:6428200-6443200	Weak transcription	Fetal Kidney	kidney
22	chr9:6429200-6462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:6429600-6449200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:6430400-6438000	Weak transcription	K562	blood
25	chr9:6431200-6449000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:6431200-6449200	Weak transcription	Adipose Nuclei	Adipose
27	chr9:6431400-6438400	Weak transcription	Brain Hippocampus Middle	brain
28	chr9:6431600-6437600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:6431600-6437800	Weak transcription	Brain Angular Gyrus	brain
30	chr9:6431600-6437800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:6431600-6438200	Weak transcription	Colon Smooth Muscle	Colon
32	chr9:6431600-6440000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:6431600-6441000	Weak transcription	Left Ventricle	heart
34	chr9:6431600-6442000	Weak transcription	Right Atrium	heart
35	chr9:6431600-6444200	Weak transcription	HSMMtube	muscle
36	chr9:6431600-6444400	Weak transcription	Right Ventricle	heart
37	chr9:6432000-6438200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:6432000-6443000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:6432800-6437800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr9:6433000-6443000	Strong transcription	Fetal Thymus	thymus
41	chr9:6433000-6444200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr9:6433200-6437600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:6433200-6439200	Weak transcription	Psoas Muscle	Psoas
44	chr9:6433400-6441400	Strong transcription	Dnd41	blood
45	chr9:6433600-6438600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:6433600-6438600	Weak transcription	Stomach Mucosa	stomach
47	chr9:6433800-6438600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr9:6433800-6438800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr9:6433800-6439600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:6434000-6438000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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