Variant report

Variant	rs10963048
Chromosome Location	chr9:17343787-17343788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10756868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810755	0.87[AFR][1000 genomes]
rs10810757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10810767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963030	0.81[AFR][1000 genomes]
rs10963031	0.88[AFR][1000 genomes]
rs10963034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963035	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963040	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs10963045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963046	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10963060	0.81[AFR][1000 genomes]
rs10963069	0.91[YRI][hapmap]
rs10963073	0.80[CEU][hapmap]
rs10963078	0.84[CEU][hapmap]
rs12156444	0.80[CEU][hapmap]
rs12378677	0.91[YRI][hapmap]
rs12553068	0.84[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553516	0.91[YRI][hapmap]
rs12555618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13285577	0.89[YRI][hapmap]
rs13293083	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301284	0.82[YRI][hapmap]
rs1348278	1.00[CEU][hapmap]
rs1442516	0.82[YRI][hapmap]
rs1442528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17829280	0.91[YRI][hapmap]
rs2151342	0.90[YRI][hapmap]
rs35409098	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4405013	0.81[YRI][hapmap]
rs62561379	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7848128	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	nsv466270	chr9:17236376-17377629	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv613694	chr9:17236376-17377629	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv892665	chr9:17250170-17371690	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv613695	chr9:17273731-17348412	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	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
13	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10963048	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17284400-17344800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:17292200-17367200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:17294000-17346000	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:17315400-17347400	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:17315400-17349800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:17319000-17349800	Weak transcription	Osteobl	bone
7	chr9:17319400-17349800	Weak transcription	NH-A	brain
8	chr9:17327000-17349800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:17327800-17346200	Weak transcription	HSMM	muscle
10	chr9:17329200-17367000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:17330200-17350200	Weak transcription	NHDF-Ad	bronchial
12	chr9:17330200-17367000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:17330400-17346000	Weak transcription	Fetal Lung	lung
14	chr9:17330600-17350800	Weak transcription	Fetal Kidney	kidney
15	chr9:17332200-17346800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:17332200-17367000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr9:17332400-17345800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:17332400-17354800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:17332400-17367600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:17332600-17343800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:17332600-17346200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:17332800-17350200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:17332800-17367400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:17333000-17343800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:17334400-17346000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr9:17334400-17353800	Weak transcription	Fetal Stomach	stomach
27	chr9:17334600-17348200	Weak transcription	Psoas Muscle	Psoas
28	chr9:17335000-17367000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:17336800-17367200	Weak transcription	Fetal Intestine Small	intestine
30	chr9:17338600-17361400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:17338800-17371800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:17339400-17344000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:17339400-17367000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:17339400-17367200	Weak transcription	Gastric	stomach
35	chr9:17339600-17349600	Weak transcription	Hela-S3	cervix
36	chr9:17339800-17344200	Strong transcription	Liver	Liver
37	chr9:17339800-17350000	Weak transcription	NHLF	lung
38	chr9:17340000-17346200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:17340000-17348000	Weak transcription	Esophagus	oesophagus
40	chr9:17340200-17349600	Weak transcription	Brain Substantia Nigra	brain
41	chr9:17340400-17344600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr9:17340400-17365600	Weak transcription	Left Ventricle	heart
43	chr9:17340800-17344000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:17341000-17348600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr9:17341000-17349200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr9:17341000-17351400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:17341200-17343800	Weak transcription	HUVEC	blood vessel
48	chr9:17341200-17348400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:17341200-17367600	Weak transcription	Spleen	Spleen
50	chr9:17341400-17367000	Weak transcription	Right Ventricle	heart

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