Variant report

Variant	rs569866
Chromosome Location	chr9:6466285-6466286
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6417367..6418926-chr9:6465280..6467264,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10115362	0.80[ASN][1000 genomes]
rs10115883	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10122116	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10124572	0.95[ASN][1000 genomes]
rs10125914	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10733529	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10739098	0.86[ASN][1000 genomes]
rs10739099	0.86[ASN][1000 genomes]
rs10739100	0.86[ASN][1000 genomes]
rs10739102	0.83[ASN][1000 genomes]
rs10758783	0.83[ASN][1000 genomes]
rs10758784	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10758785	0.83[ASN][1000 genomes]
rs10758786	0.85[ASN][1000 genomes]
rs10758787	0.85[ASN][1000 genomes]
rs10758788	0.86[ASN][1000 genomes]
rs10758789	0.85[ASN][1000 genomes]
rs10758790	0.85[ASN][1000 genomes]
rs10758791	0.84[ASN][1000 genomes]
rs10758792	0.89[ASN][1000 genomes]
rs10815435	0.83[ASN][1000 genomes]
rs10975582	0.81[ASN][1000 genomes]
rs10975583	0.85[ASN][1000 genomes]
rs10975585	0.89[ASN][1000 genomes]
rs10975595	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10975603	0.86[ASN][1000 genomes]
rs10975605	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1156747	0.89[ASN][1000 genomes]
rs11790625	0.93[ASN][1000 genomes]
rs11791651	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11795355	0.86[ASN][1000 genomes]
rs12346455	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12347573	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12351293	0.95[ASN][1000 genomes]
rs12376117	0.81[ASN][1000 genomes]
rs13283381	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13289925	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13291472	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13292799	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13296970	0.90[EUR][1000 genomes]
rs13301146	0.90[EUR][1000 genomes]
rs13440427	0.91[ASN][1000 genomes]
rs1381035	0.84[ASN][1000 genomes]
rs1381036	0.84[ASN][1000 genomes]
rs1381037	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16924562	0.91[ASN][1000 genomes]
rs16924591	0.97[ASN][1000 genomes]
rs16924624	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16924626	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16924631	0.86[ASN][1000 genomes]
rs1824537	0.83[ASN][1000 genomes]
rs1870696	0.93[ASN][1000 genomes]
rs1903419	0.84[ASN][1000 genomes]
rs2065074	0.83[ASN][1000 genomes]
rs2065075	0.84[ASN][1000 genomes]
rs2169283	0.81[ASN][1000 genomes]
rs2169286	0.89[ASN][1000 genomes]
rs3739654	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs380674	0.81[ASN][1000 genomes]
rs4380997	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4384035	0.98[ASN][1000 genomes]
rs4463484	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4556138	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4740844	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4740845	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4742199	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4742201	0.85[ASN][1000 genomes]
rs4742202	0.85[ASN][1000 genomes]
rs4742204	0.82[ASN][1000 genomes]
rs504698	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530722	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55960819	0.97[ASN][1000 genomes]
rs56218473	0.87[ASN][1000 genomes]
rs56396114	0.95[ASN][1000 genomes]
rs56939673	0.86[ASN][1000 genomes]
rs6477086	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6477087	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66509816	0.85[ASN][1000 genomes]
rs67852216	0.80[ASN][1000 genomes]
rs7027302	0.97[ASN][1000 genomes]
rs7029772	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7033940	0.85[ASN][1000 genomes]
rs7034328	0.89[ASN][1000 genomes]
rs73399080	0.87[ASN][1000 genomes]
rs73401025	0.83[ASN][1000 genomes]
rs73401679	0.86[ASN][1000 genomes]
rs7847675	0.81[ASN][1000 genomes]
rs7848831	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7852539	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7853059	0.86[ASN][1000 genomes]
rs7853834	0.86[ASN][1000 genomes]
rs7857628	0.80[ASN][1000 genomes]
rs7860427	0.80[ASN][1000 genomes]
rs7860966	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7861073	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7861559	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7865955	0.83[ASN][1000 genomes]
rs7871134	0.83[ASN][1000 genomes]
rs7873756	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7876000	0.88[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
rs569866	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
2	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
3	chr9:6435400-6482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:6438000-6477600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr9:6441600-6475200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr9:6443600-6477600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:6446800-6468200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:6449400-6467400	Weak transcription	Spleen	Spleen
9	chr9:6450000-6466800	Weak transcription	Liver	Liver
10	chr9:6450000-6467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:6450000-6471200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:6450000-6473600	Weak transcription	Small Intestine	intestine
13	chr9:6450000-6477600	Weak transcription	Left Ventricle	heart
14	chr9:6450000-6477600	Weak transcription	HSMMtube	muscle
15	chr9:6450000-6477600	Weak transcription	NHLF	lung
16	chr9:6450000-6478600	Weak transcription	Ovary	ovary
17	chr9:6450000-6482800	Weak transcription	Pancreas	Pancrea
18	chr9:6450200-6467000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:6450200-6477400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:6450600-6468400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr9:6450800-6477400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:6451000-6466600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:6451000-6466800	Weak transcription	A549	lung
24	chr9:6451000-6471200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:6451000-6477600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:6451200-6472000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:6451200-6475800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr9:6451200-6477600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:6452600-6488000	Weak transcription	Colon Smooth Muscle	Colon
30	chr9:6452800-6472200	Weak transcription	Fetal Heart	heart
31	chr9:6452800-6476000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:6452800-6481600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:6452800-6485400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr9:6452800-6485400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:6454600-6466600	Weak transcription	NHEK	skin
36	chr9:6456000-6471200	Weak transcription	Thymus	Thymus
37	chr9:6456200-6477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:6456200-6477800	Weak transcription	Fetal Brain Female	brain
39	chr9:6458600-6476000	Weak transcription	Fetal Muscle Leg	muscle
40	chr9:6458600-6482800	Weak transcription	Gastric	stomach
41	chr9:6458800-6467600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:6458800-6497200	Weak transcription	Colonic Mucosa	Colon
43	chr9:6459000-6477600	Weak transcription	Fetal Kidney	kidney
44	chr9:6459200-6469200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:6459200-6477600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr9:6459200-6477800	Weak transcription	Brain Germinal Matrix	brain
47	chr9:6459400-6501800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:6459600-6469200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr9:6460000-6467000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:6460000-6467400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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