Variant report

Variant	rs10118449
Chromosome Location	chr9:6515433-6515434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10975622	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12352034	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13297368	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13298500	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16924650	0.81[ASN][1000 genomes]
rs34551978	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34806087	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35458135	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7848483	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[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	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	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
9	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
10	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
11	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
12	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
13	esv2761298	chr9:6505897-6544766	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10118449	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6463600-6518400	Weak transcription	Fetal Brain Male	brain
2	chr9:6498800-6554400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:6499000-6528400	Weak transcription	Pancreas	Pancrea
4	chr9:6500800-6517400	Weak transcription	Esophagus	oesophagus
5	chr9:6505600-6517200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:6506200-6518600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:6506400-6517200	Weak transcription	Lung	lung
8	chr9:6506400-6521800	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:6506400-6530600	Weak transcription	Gastric	stomach
10	chr9:6506800-6519200	Weak transcription	Fetal Kidney	kidney
11	chr9:6507000-6515800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:6507000-6523800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr9:6507000-6524800	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:6507000-6534400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:6507200-6522400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:6507800-6521800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr9:6508000-6516000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:6508000-6517400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:6508000-6520200	Weak transcription	Fetal Intestine Small	intestine
20	chr9:6508200-6519400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr9:6508200-6521800	Weak transcription	Fetal Stomach	stomach
22	chr9:6508400-6519600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr9:6508400-6521000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:6508400-6521800	Weak transcription	Primary B cells from cord blood	blood
25	chr9:6508400-6523600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:6508400-6525000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:6508400-6526400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:6508400-6526600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr9:6508400-6528200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:6508400-6530600	Weak transcription	Left Ventricle	heart
31	chr9:6508600-6524200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:6508600-6537800	Weak transcription	HMEC	breast
33	chr9:6508600-6538200	Weak transcription	NHEK	skin
34	chr9:6508800-6517400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr9:6508800-6518600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:6508800-6519000	Weak transcription	Dnd41	blood
37	chr9:6508800-6520200	Weak transcription	Fetal Muscle Leg	muscle
38	chr9:6508800-6521400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:6508800-6521800	Weak transcription	GM12878-XiMat	blood
40	chr9:6508800-6523800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr9:6508800-6526600	Weak transcription	HSMM	muscle
42	chr9:6509000-6519200	Weak transcription	Fetal Intestine Large	intestine
43	chr9:6509000-6520200	Weak transcription	Liver	Liver
44	chr9:6509000-6521600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:6509000-6521800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:6509000-6521800	Weak transcription	Adipose Nuclei	Adipose
47	chr9:6509400-6521800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:6509600-6517200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:6509800-6525000	Weak transcription	Osteobl	bone
50	chr9:6509800-6530200	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links