Variant report

Variant	rs1824537
Chromosome Location	chr9:6430182-6430183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6411987..6416661-chr9:6426661..6431000,5	K562	blood:
2	chr9:6411987..6414825-chr9:6429443..6431000,2	K562	blood:

Variant related genes	Relation type
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10115362	0.84[ASN][1000 genomes]
rs10124572	0.88[ASN][1000 genomes]
rs10733529	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739098	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739099	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739100	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739102	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758783	0.83[ASN][1000 genomes]
rs10758784	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10758785	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10758786	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758787	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758788	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758789	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758790	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758791	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10758792	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815428	0.83[ASN][1000 genomes]
rs10815435	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10975579	0.88[ASN][1000 genomes]
rs10975582	0.90[ASN][1000 genomes]
rs10975583	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10975585	0.93[ASN][1000 genomes]
rs10975595	0.88[ASN][1000 genomes]
rs1156747	0.92[ASN][1000 genomes]
rs11790625	0.89[ASN][1000 genomes]
rs11791651	0.83[ASN][1000 genomes]
rs12346455	0.84[ASN][1000 genomes]
rs12351293	0.88[ASN][1000 genomes]
rs12376117	0.83[ASN][1000 genomes]
rs13292799	0.90[ASN][1000 genomes]
rs13440427	0.84[ASN][1000 genomes]
rs1381035	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381036	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381037	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16924562	0.87[ASN][1000 genomes]
rs16924591	0.85[ASN][1000 genomes]
rs1870696	0.86[ASN][1000 genomes]
rs1903419	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065074	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2065075	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2169283	0.89[ASN][1000 genomes]
rs2169286	0.93[ASN][1000 genomes]
rs2381444	0.88[ASN][1000 genomes]
rs3739654	0.83[ASN][1000 genomes]
rs380674	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs394137	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs414107	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4380997	0.81[ASN][1000 genomes]
rs4384035	0.86[ASN][1000 genomes]
rs452135	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4556138	0.83[ASN][1000 genomes]
rs4740844	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4740845	0.96[ASN][1000 genomes]
rs4742199	0.94[ASN][1000 genomes]
rs4742201	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742202	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742204	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs504698	0.85[ASN][1000 genomes]
rs530722	0.83[ASN][1000 genomes]
rs55960819	0.86[ASN][1000 genomes]
rs56218473	0.93[ASN][1000 genomes]
rs56396114	0.88[ASN][1000 genomes]
rs56939673	0.88[ASN][1000 genomes]
rs569866	0.83[ASN][1000 genomes]
rs6477086	0.81[ASN][1000 genomes]
rs67852216	0.84[ASN][1000 genomes]
rs7027302	0.86[ASN][1000 genomes]
rs7033940	0.87[ASN][1000 genomes]
rs73401679	0.86[ASN][1000 genomes]
rs7853059	0.86[ASN][1000 genomes]
rs7853834	0.86[ASN][1000 genomes]
rs7857628	0.83[ASN][1000 genomes]
rs7860427	0.84[ASN][1000 genomes]
rs7860966	0.92[ASN][1000 genomes]
rs7861073	0.92[ASN][1000 genomes]
rs7861559	0.92[ASN][1000 genomes]
rs7865955	0.83[ASN][1000 genomes]
rs7871134	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1824537	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	chr9:6415400-6434000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:6415600-6431000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:6415600-6441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
10	chr9:6415800-6442800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:6416000-6438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:6416400-6430600	Weak transcription	Right Ventricle	heart
13	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:6417400-6434400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:6417600-6430600	Weak transcription	HSMM	muscle
16	chr9:6417600-6437800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:6417800-6440000	Weak transcription	Fetal Brain Female	brain
18	chr9:6418000-6438200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:6418800-6430600	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:6419000-6437000	Weak transcription	Fetal Brain Male	brain
21	chr9:6419200-6430600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:6419200-6433800	Weak transcription	Brain Substantia Nigra	brain
23	chr9:6419200-6437800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:6419400-6432200	Weak transcription	Brain Anterior Caudate	brain
25	chr9:6419400-6437400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:6420400-6430600	Weak transcription	Ovary	ovary
27	chr9:6420800-6430400	Weak transcription	Small Intestine	intestine
28	chr9:6421400-6449400	Weak transcription	Liver	Liver
29	chr9:6421800-6430200	Weak transcription	Left Ventricle	heart
30	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
31	chr9:6422800-6430400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:6422800-6430600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr9:6422800-6434000	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:6422800-6434200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:6422800-6446400	Weak transcription	Brain Germinal Matrix	brain
36	chr9:6422800-6449200	Weak transcription	Pancreas	Pancrea
37	chr9:6423400-6440800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr9:6423800-6434000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr9:6425400-6430600	Weak transcription	Adipose Nuclei	Adipose
40	chr9:6425400-6433800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr9:6425800-6434000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr9:6426000-6433600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:6426200-6434000	Weak transcription	Fetal Intestine Large	intestine
44	chr9:6426200-6439800	Weak transcription	NHLF	lung
45	chr9:6426400-6430600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr9:6426400-6436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr9:6426600-6430600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr9:6426600-6430800	Weak transcription	NH-A	brain
49	chr9:6426600-6431200	Weak transcription	HSMMtube	muscle
50	chr9:6426600-6433200	Weak transcription	A549	lung

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