Variant report

Variant	rs2065074
Chromosome Location	chr9:6420225-6420226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:6412168..6415418-chr9:6418500..6425043,7	MCF-7	breast:
2	chr9:6417292..6420636-chr9:6422611..6425827,4	K562	blood:
3	chr9:6417900..6420636-chr9:6424327..6426106,2	K562	blood:
4	chr9:6413231..6415998-chr9:6419721..6423966,4	MCF-7	breast:

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	0.83[ASN][1000 genomes]
rs10124572	0.86[ASN][1000 genomes]
rs10733529	0.94[ASN][1000 genomes]
rs10739098	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739099	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739100	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739102	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758783	0.83[ASN][1000 genomes]
rs10758784	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10758785	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10758786	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758787	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758788	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758789	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758790	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758791	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10758792	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10815428	0.83[ASN][1000 genomes]
rs10815435	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10975579	0.87[ASN][1000 genomes]
rs10975582	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10975583	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10975585	0.90[ASN][1000 genomes]
rs10975595	0.86[ASN][1000 genomes]
rs1156747	0.91[ASN][1000 genomes]
rs11790625	0.87[ASN][1000 genomes]
rs11791651	0.83[ASN][1000 genomes]
rs12346455	0.83[ASN][1000 genomes]
rs12351293	0.86[ASN][1000 genomes]
rs12376117	0.83[ASN][1000 genomes]
rs13292799	0.88[ASN][1000 genomes]
rs13440427	0.82[ASN][1000 genomes]
rs1381035	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381036	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381037	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16924562	0.85[ASN][1000 genomes]
rs16924591	0.84[ASN][1000 genomes]
rs1824537	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1870696	0.84[ASN][1000 genomes]
rs1903419	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065075	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2169283	0.89[ASN][1000 genomes]
rs2169286	0.90[ASN][1000 genomes]
rs2381444	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3739654	0.83[ASN][1000 genomes]
rs380674	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs394137	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs414107	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4380997	0.81[ASN][1000 genomes]
rs4384035	0.85[ASN][1000 genomes]
rs452135	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4556138	0.82[ASN][1000 genomes]
rs4740844	0.94[ASN][1000 genomes]
rs4740845	0.94[ASN][1000 genomes]
rs4742199	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4742201	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742202	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742204	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs504698	0.84[ASN][1000 genomes]
rs530722	0.83[ASN][1000 genomes]
rs55960819	0.86[ASN][1000 genomes]
rs56218473	0.94[ASN][1000 genomes]
rs56396114	0.86[ASN][1000 genomes]
rs56939673	0.87[ASN][1000 genomes]
rs569866	0.83[ASN][1000 genomes]
rs6477086	0.81[ASN][1000 genomes]
rs67852216	0.83[ASN][1000 genomes]
rs7027302	0.86[ASN][1000 genomes]
rs7033940	0.85[ASN][1000 genomes]
rs73401679	0.84[ASN][1000 genomes]
rs7853059	0.84[ASN][1000 genomes]
rs7853834	0.84[ASN][1000 genomes]
rs7857628	0.82[ASN][1000 genomes]
rs7860427	0.83[ASN][1000 genomes]
rs7860966	0.90[ASN][1000 genomes]
rs7861073	0.90[ASN][1000 genomes]
rs7861559	0.90[ASN][1000 genomes]
rs7865955	0.83[ASN][1000 genomes]
rs7871134	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[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
rs2065074	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	chr9:6414400-6427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:6414600-6439400	Weak transcription	Colonic Mucosa	Colon
3	chr9:6414600-6449000	Weak transcription	Gastric	stomach
4	chr9:6414600-6449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
6	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
7	chr9:6414800-6422000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:6415400-6425400	Weak transcription	Psoas Muscle	Psoas
9	chr9:6415400-6434000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr9:6415600-6420800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:6415600-6421000	Weak transcription	Fetal Intestine Large	intestine
12	chr9:6415600-6422000	Weak transcription	Fetal Kidney	kidney
13	chr9:6415600-6422200	Weak transcription	Lung	lung
14	chr9:6415600-6423200	Weak transcription	Stomach Mucosa	stomach
15	chr9:6415600-6430000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:6415600-6431000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:6415600-6441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
19	chr9:6415800-6442800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:6416000-6438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:6416400-6420600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:6416400-6421400	Weak transcription	Left Ventricle	heart
23	chr9:6416400-6421400	Weak transcription	Pancreas	Pancrea
24	chr9:6416400-6429800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:6416400-6430000	Weak transcription	Spleen	Spleen
26	chr9:6416400-6430600	Weak transcription	Right Ventricle	heart
27	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:6416600-6421400	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:6417000-6422200	Weak transcription	Fetal Stomach	stomach
30	chr9:6417200-6422200	Weak transcription	Brain Germinal Matrix	brain
31	chr9:6417400-6420800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr9:6417400-6424600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:6417400-6434400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:6417600-6421400	Weak transcription	Fetal Lung	lung
35	chr9:6417600-6430600	Weak transcription	HSMM	muscle
36	chr9:6417600-6437800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:6417800-6420800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:6417800-6420800	Weak transcription	Liver	Liver
39	chr9:6417800-6421000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:6417800-6421200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:6417800-6422200	Weak transcription	NHLF	lung
42	chr9:6417800-6425800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr9:6417800-6426000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr9:6417800-6428600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:6417800-6428800	Weak transcription	K562	blood
46	chr9:6417800-6440000	Weak transcription	Fetal Brain Female	brain
47	chr9:6418000-6420800	Weak transcription	Dnd41	blood
48	chr9:6418000-6420800	Weak transcription	HMEC	breast
49	chr9:6418000-6421000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:6418000-6421400	Weak transcription	Thymus	Thymus

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