Variant report

Variant	rs394137
Chromosome Location	chr9:6440619-6440620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10115883	0.82[YRI][hapmap]
rs10733529	0.82[ASN][1000 genomes]
rs10739098	0.94[CEU][hapmap];0.81[CHB][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10739099	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10739100	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10739102	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10758784	0.88[CEU][hapmap];0.81[CHB][hapmap];0.92[YRI][hapmap]
rs10758785	0.94[CEU][hapmap];0.81[CHB][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10758786	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10758787	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10758788	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10758789	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10758790	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10758791	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10758792	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10815435	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10975582	0.83[AMR][1000 genomes]
rs10975583	0.94[CEU][hapmap];0.81[CHB][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10975595	0.88[CEU][hapmap];0.84[ASN][1000 genomes]
rs10975605	0.82[YRI][hapmap]
rs1156747	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs11790625	0.81[ASN][1000 genomes]
rs12346455	0.83[CEU][hapmap]
rs12347573	0.83[YRI][hapmap]
rs13291472	0.83[CEU][hapmap]
rs13292799	0.82[ASN][1000 genomes]
rs1381035	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1381036	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1381037	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16924562	0.83[ASN][1000 genomes]
rs1824537	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1870696	0.81[ASN][1000 genomes]
rs1903419	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2065074	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2065075	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2169283	0.80[AMR][1000 genomes]
rs2169286	0.81[CHB][hapmap]
rs2381444	0.82[AMR][1000 genomes]
rs3739654	0.83[CEU][hapmap]
rs380674	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs414107	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452135	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4740844	0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs4740845	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4742199	0.81[ASN][1000 genomes]
rs4742201	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742202	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742204	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56218473	0.81[ASN][1000 genomes]
rs6477087	0.81[YRI][hapmap]
rs7033570	0.91[ASN][1000 genomes]
rs7033940	0.89[ASN][1000 genomes]
rs73401679	0.87[ASN][1000 genomes]
rs7852539	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs7853059	0.87[ASN][1000 genomes]
rs7853834	0.87[ASN][1000 genomes]
rs7857628	0.81[CHB][hapmap]
rs7860966	0.83[ASN][1000 genomes]
rs7861073	0.83[ASN][1000 genomes]
rs7861559	0.83[ASN][1000 genomes]
rs7865955	0.81[CHB][hapmap];0.80[YRI][hapmap]
rs7871134	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[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
rs394137	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6449000	Weak transcription	Gastric	stomach
2	chr9:6414600-6449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
4	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
5	chr9:6415600-6441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
7	chr9:6415800-6442800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:6421400-6449400	Weak transcription	Liver	Liver
10	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
11	chr9:6422800-6446400	Weak transcription	Brain Germinal Matrix	brain
12	chr9:6422800-6449200	Weak transcription	Pancreas	Pancrea
13	chr9:6423400-6440800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:6428200-6443200	Weak transcription	Fetal Kidney	kidney
15	chr9:6429200-6462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:6429600-6449200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:6431200-6449000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr9:6431200-6449200	Weak transcription	Adipose Nuclei	Adipose
19	chr9:6431600-6441000	Weak transcription	Left Ventricle	heart
20	chr9:6431600-6442000	Weak transcription	Right Atrium	heart
21	chr9:6431600-6444200	Weak transcription	HSMMtube	muscle
22	chr9:6431600-6444400	Weak transcription	Right Ventricle	heart
23	chr9:6432000-6443000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:6433000-6443000	Strong transcription	Fetal Thymus	thymus
25	chr9:6433000-6444200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:6433400-6441400	Strong transcription	Dnd41	blood
27	chr9:6434400-6449200	Weak transcription	A549	lung
28	chr9:6434600-6441400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:6434800-6447200	Weak transcription	Brain Anterior Caudate	brain
30	chr9:6435000-6441200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:6435000-6460400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr9:6435000-6463800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:6435200-6441200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:6435400-6441000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:6435400-6444600	Weak transcription	Lung	lung
36	chr9:6435400-6482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr9:6435800-6441000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:6435800-6444800	Weak transcription	Fetal Intestine Large	intestine
39	chr9:6436000-6447800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:6436200-6441400	Weak transcription	Osteobl	bone
41	chr9:6436200-6443600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:6436400-6443400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr9:6436400-6445200	Weak transcription	Thymus	Thymus
44	chr9:6436600-6449200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:6436800-6440800	Weak transcription	NHDF-Ad	bronchial
46	chr9:6437000-6447400	Weak transcription	HSMM	muscle
47	chr9:6437000-6447800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr9:6437200-6442800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:6437600-6441000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:6437800-6441400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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