Variant report

Variant	rs7848831
Chromosome Location	chr9:6504049-6504050
allele	C/G
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]
rs10125914	0.81[AMR][1000 genomes]
rs10733529	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10758784	0.86[EUR][1000 genomes]
rs10975595	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10975622	0.80[EUR][1000 genomes]
rs12346455	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12347573	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12352034	0.82[AMR][1000 genomes]
rs13283381	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13289925	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13291472	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13292799	0.86[EUR][1000 genomes]
rs13296970	0.89[EUR][1000 genomes]
rs13298500	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13301146	0.89[EUR][1000 genomes]
rs16924624	0.81[ASN][1000 genomes]
rs16924631	0.85[ASN][1000 genomes]
rs16924634	0.82[ASN][1000 genomes]
rs33962342	0.83[ASN][1000 genomes]
rs3739654	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4556138	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4740844	0.84[EUR][1000 genomes]
rs4740845	0.84[EUR][1000 genomes]
rs4742199	0.83[EUR][1000 genomes]
rs504698	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs530722	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs569866	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6477086	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6477087	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66509816	0.84[ASN][1000 genomes]
rs7029772	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73401025	0.86[ASN][1000 genomes]
rs7847675	0.88[ASN][1000 genomes]
rs7852539	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7860966	0.87[EUR][1000 genomes]
rs7861073	0.87[EUR][1000 genomes]
rs7861559	0.87[EUR][1000 genomes]
rs7873756	0.87[AMR][1000 genomes];0.91[EUR][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	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
12	nsv892162	chr9:6480005-6788085	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
13	nsv831498	chr9:6496021-6689728	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7848831	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6463600-6518400	Weak transcription	Fetal Brain Male	brain
2	chr9:6471600-6504600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:6472200-6508200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:6473800-6506200	Weak transcription	Small Intestine	intestine
5	chr9:6475400-6508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:6475400-6508400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:6475400-6508800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr9:6475400-6508800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr9:6475800-6509000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:6475800-6510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:6476000-6509400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:6477600-6507800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:6477800-6511000	Weak transcription	Fetal Heart	heart
14	chr9:6480200-6508400	Weak transcription	Stomach Mucosa	stomach
15	chr9:6487600-6510600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr9:6492800-6508800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:6493000-6509000	Strong transcription	Adipose Nuclei	Adipose
18	chr9:6493400-6508400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr9:6493600-6507400	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:6493800-6506000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:6493800-6508200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr9:6494000-6508800	Strong transcription	GM12878-XiMat	blood
23	chr9:6495000-6506400	Strong transcription	HepG2	liver
24	chr9:6495000-6508400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:6495200-6510800	Strong transcription	Fetal Thymus	thymus
26	chr9:6495400-6510200	Strong transcription	HUVEC	blood vessel
27	chr9:6495400-6510600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:6495400-6511400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:6496400-6508200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:6496800-6508400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr9:6497600-6504600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr9:6497600-6505800	Weak transcription	Brain Substantia Nigra	brain
33	chr9:6497800-6505600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:6498800-6504400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:6498800-6505800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr9:6498800-6505800	Weak transcription	Brain Hippocampus Middle	brain
37	chr9:6498800-6507800	Weak transcription	Psoas Muscle	Psoas
38	chr9:6498800-6554400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:6499000-6505200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:6499000-6505400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:6499000-6505400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:6499000-6505400	Weak transcription	Gastric	stomach
43	chr9:6499000-6505800	Weak transcription	Brain Angular Gyrus	brain
44	chr9:6499000-6505800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr9:6499000-6506000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:6499000-6506600	Weak transcription	K562	blood
47	chr9:6499000-6511400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:6499000-6528400	Weak transcription	Pancreas	Pancrea
49	chr9:6499200-6506600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:6499600-6506200	Strong transcription	NHDF-Ad	bronchial

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