Variant report

Variant	rs34105027
Chromosome Location	chr9:17413208-17413209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 188 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:171)

rs_ID	r²[population]
rs10046851	0.90[EUR][1000 genomes]
rs10114083	0.91[EUR][1000 genomes]
rs10114662	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10114688	0.90[EUR][1000 genomes]
rs10114730	0.90[EUR][1000 genomes]
rs10116093	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10116140	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10116428	0.90[EUR][1000 genomes]
rs10119297	0.90[EUR][1000 genomes]
rs10119370	0.90[EUR][1000 genomes]
rs10120757	0.90[EUR][1000 genomes]
rs10121841	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10122987	0.91[EUR][1000 genomes]
rs10123109	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10123715	0.90[EUR][1000 genomes]
rs10123745	0.91[EUR][1000 genomes]
rs10124487	0.94[EUR][1000 genomes]
rs10124513	0.90[EUR][1000 genomes]
rs10125333	0.90[EUR][1000 genomes]
rs10283690	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10481559	0.90[EUR][1000 genomes]
rs10738474	0.91[EUR][1000 genomes]
rs10738476	0.91[EUR][1000 genomes]
rs10756860	0.87[EUR][1000 genomes]
rs10756866	0.89[EUR][1000 genomes]
rs10756867	0.89[EUR][1000 genomes]
rs10756869	0.94[EUR][1000 genomes]
rs10756874	0.91[EUR][1000 genomes]
rs10756875	0.91[EUR][1000 genomes]
rs10756876	0.91[EUR][1000 genomes]
rs10756877	0.91[EUR][1000 genomes]
rs10756878	0.93[EUR][1000 genomes]
rs10810748	0.84[EUR][1000 genomes]
rs10810749	0.84[EUR][1000 genomes]
rs10810750	0.85[EUR][1000 genomes]
rs10810751	0.85[EUR][1000 genomes]
rs10810752	0.85[EUR][1000 genomes]
rs10810756	0.89[EUR][1000 genomes]
rs10810761	0.94[EUR][1000 genomes]
rs10810763	0.90[EUR][1000 genomes]
rs10810764	0.90[EUR][1000 genomes]
rs10810765	0.90[EUR][1000 genomes]
rs10810773	0.91[EUR][1000 genomes]
rs10810774	0.91[EUR][1000 genomes]
rs10810775	0.91[EUR][1000 genomes]
rs10810777	0.91[EUR][1000 genomes]
rs10810781	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10810782	0.85[EUR][1000 genomes]
rs10962950	0.81[EUR][1000 genomes]
rs10963026	0.85[EUR][1000 genomes]
rs10963042	0.90[EUR][1000 genomes]
rs10963057	0.89[EUR][1000 genomes]
rs10963063	0.94[EUR][1000 genomes]
rs12337154	0.88[EUR][1000 genomes]
rs12337171	0.92[EUR][1000 genomes]
rs12339564	0.86[EUR][1000 genomes]
rs12342180	0.91[EUR][1000 genomes]
rs12345267	0.85[EUR][1000 genomes]
rs12379102	0.91[EUR][1000 genomes]
rs12379104	0.85[EUR][1000 genomes]
rs13290922	0.83[EUR][1000 genomes]
rs1372702	0.91[EUR][1000 genomes]
rs1442523	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1442524	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1442533	0.86[EUR][1000 genomes]
rs1583987	0.89[EUR][1000 genomes]
rs1596193	0.94[EUR][1000 genomes]
rs1759454	0.84[EUR][1000 genomes]
rs1759613	0.85[EUR][1000 genomes]
rs1889114	0.86[EUR][1000 genomes]
rs1953105	0.81[EUR][1000 genomes]
rs2044119	0.89[EUR][1000 genomes]
rs2044120	0.89[EUR][1000 genomes]
rs2099858	0.91[EUR][1000 genomes]
rs2225598	0.91[EUR][1000 genomes]
rs2584547	0.84[EUR][1000 genomes]
rs2584553	0.82[EUR][1000 genomes]
rs2584554	0.81[EUR][1000 genomes]
rs2593387	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2779773	0.86[EUR][1000 genomes]
rs2779775	0.82[EUR][1000 genomes]
rs2779776	0.82[EUR][1000 genomes]
rs2780197	0.82[EUR][1000 genomes]
rs2780201	0.83[EUR][1000 genomes]
rs2780209	0.85[EUR][1000 genomes]
rs2780212	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2990670	0.83[EUR][1000 genomes]
rs36057268	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3765040	0.90[EUR][1000 genomes]
rs3780258	0.85[EUR][1000 genomes]
rs3808784	0.90[EUR][1000 genomes]
rs3824391	0.90[EUR][1000 genomes]
rs3824392	0.90[EUR][1000 genomes]
rs3861711	0.91[EUR][1000 genomes]
rs4246135	0.90[EUR][1000 genomes]
rs4246136	0.90[EUR][1000 genomes]
rs4272484	0.92[EUR][1000 genomes]
rs4409489	0.85[EUR][1000 genomes]
rs4563978	0.94[EUR][1000 genomes]
rs4961437	0.91[EUR][1000 genomes]
rs4961439	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4961539	0.90[EUR][1000 genomes]
rs4961540	0.90[EUR][1000 genomes]
rs4961541	0.91[EUR][1000 genomes]
rs4961542	0.91[EUR][1000 genomes]
rs4961543	0.91[EUR][1000 genomes]
rs4961544	0.90[EUR][1000 genomes]
rs4961545	0.91[EUR][1000 genomes]
rs4961547	0.91[EUR][1000 genomes]
rs4961548	0.90[EUR][1000 genomes]
rs4961552	0.91[EUR][1000 genomes]
rs4961553	0.91[EUR][1000 genomes]
rs4961555	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4961557	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593614	0.87[EUR][1000 genomes]
rs595894	0.85[EUR][1000 genomes]
rs605916	0.84[EUR][1000 genomes]
rs619380	0.84[EUR][1000 genomes]
rs632265	0.84[EUR][1000 genomes]
rs645117	0.86[EUR][1000 genomes]
rs6475139	0.91[EUR][1000 genomes]
rs6475141	0.90[EUR][1000 genomes]
rs6475142	0.89[EUR][1000 genomes]
rs6475143	0.90[EUR][1000 genomes]
rs6475144	0.90[EUR][1000 genomes]
rs6475145	0.90[EUR][1000 genomes]
rs6475147	0.82[EUR][1000 genomes]
rs654521	0.82[EUR][1000 genomes]
rs670058	0.87[EUR][1000 genomes]
rs670511	0.84[EUR][1000 genomes]
rs7022024	0.90[EUR][1000 genomes]
rs7022060	0.94[EUR][1000 genomes]
rs7028593	0.90[EUR][1000 genomes]
rs7028779	0.90[EUR][1000 genomes]
rs7028930	0.90[EUR][1000 genomes]
rs7031133	0.90[EUR][1000 genomes]
rs7037111	0.94[EUR][1000 genomes]
rs7038064	0.91[EUR][1000 genomes]
rs7038186	0.86[EUR][1000 genomes]
rs7038197	0.90[EUR][1000 genomes]
rs7041840	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7044462	0.85[EUR][1000 genomes]
rs7044823	0.90[EUR][1000 genomes]
rs7046933	0.81[EUR][1000 genomes]
rs7848397	0.91[EUR][1000 genomes]
rs7848980	0.91[EUR][1000 genomes]
rs7849084	0.84[EUR][1000 genomes]
rs7849085	0.84[EUR][1000 genomes]
rs7851890	0.90[EUR][1000 genomes]
rs7854724	0.89[EUR][1000 genomes]
rs7854802	0.90[EUR][1000 genomes]
rs7854818	0.89[EUR][1000 genomes]
rs7862069	0.91[EUR][1000 genomes]
rs7864270	0.89[EUR][1000 genomes]
rs7864271	0.89[EUR][1000 genomes]
rs7864650	0.85[EUR][1000 genomes]
rs7864919	0.91[EUR][1000 genomes]
rs7865766	0.93[EUR][1000 genomes]
rs7868684	0.82[EUR][1000 genomes]
rs7868700	0.89[EUR][1000 genomes]
rs7869727	0.90[EUR][1000 genomes]
rs7870101	0.90[EUR][1000 genomes]
rs7871926	0.89[EUR][1000 genomes]
rs7872831	0.89[EUR][1000 genomes]
rs7873708	0.90[EUR][1000 genomes]
rs7874453	0.90[EUR][1000 genomes]
rs870271	0.86[EUR][1000 genomes]
rs9298772	0.89[EUR][1000 genomes]
rs9298773	0.90[EUR][1000 genomes]
rs9298774	0.90[EUR][1000 genomes]
rs9695844	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv466271	chr9:17329964-17438391	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv613696	chr9:17329964-17438391	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1015524	chr9:17350843-17419424	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv892668	chr9:17371690-17532840	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv892669	chr9:17378776-17438391	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv892670	chr9:17378776-17507277	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv892671	chr9:17378776-17610211	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv466273	chr9:17391531-17436662	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv613697	chr9:17391531-17436662	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv523411	chr9:17394536-17454799	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv2422265	chr9:17396711-17598187	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34105027	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17368400-17457800	Weak transcription	Pancreas	Pancrea
2	chr9:17381400-17422800	Weak transcription	Colon Smooth Muscle	Colon
3	chr9:17393400-17433000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr9:17395400-17413600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:17395400-17417800	Weak transcription	NHDF-Ad	bronchial
6	chr9:17396200-17440000	Weak transcription	Adipose Nuclei	Adipose
7	chr9:17398800-17430600	Weak transcription	HSMM	muscle
8	chr9:17399400-17425400	Weak transcription	Fetal Heart	heart
9	chr9:17408000-17437200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:17409600-17425400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:17411600-17428000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:17411800-17414000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:17411800-17416000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:17411800-17418200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:17411800-17423400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:17411800-17423400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:17411800-17428800	Weak transcription	Lung	lung
18	chr9:17411800-17429200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr9:17411800-17432200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:17411800-17434400	Weak transcription	Dnd41	blood
21	chr9:17411800-17435600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:17411800-17439800	Weak transcription	Left Ventricle	heart
23	chr9:17411800-17481000	Weak transcription	Aorta	Aorta
24	chr9:17412000-17414200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:17412000-17427600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:17412000-17428000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:17412200-17413800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:17412200-17418200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:17412200-17418400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:17412200-17419800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:17412200-17422800	Weak transcription	Fetal Lung	lung
32	chr9:17412200-17423000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:17412200-17424800	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:17412200-17425200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr9:17412200-17440200	Weak transcription	Fetal Stomach	stomach
36	chr9:17412200-17443600	Weak transcription	Ovary	ovary
37	chr9:17412400-17419600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr9:17412400-17430800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:17412600-17415600	Weak transcription	Liver	Liver

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