Variant report

Variant	rs7029772
Chromosome Location	chr9:6497589-6497590
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6412621..6414719-chr9:6496485..6499094,2	K562	blood:

Variant related genes	Relation type
ENSG00000147854	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10115883	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10122116	0.94[CHB][hapmap]
rs10733529	0.80[EUR][1000 genomes]
rs10739098	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs10739099	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10758784	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs10758785	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs10758788	0.82[CHB][hapmap]
rs10758789	0.87[CHB][hapmap]
rs10758790	0.82[CHB][hapmap]
rs10815428	0.84[JPT][hapmap]
rs10975583	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs10975595	0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs10975605	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs1156747	0.82[CHB][hapmap]
rs11791651	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs11795355	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs12346455	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs12347573	0.87[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13283381	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13289925	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13291472	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13292799	0.80[EUR][1000 genomes]
rs13296970	0.86[EUR][1000 genomes]
rs13298500	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13301146	0.86[EUR][1000 genomes]
rs16924562	0.94[CHB][hapmap]
rs16924624	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs16924626	0.94[CHB][hapmap]
rs16924631	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs16924634	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1870696	0.94[CHB][hapmap]
rs1903419	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2169283	0.88[CHB][hapmap]
rs2169286	0.82[CHB][hapmap]
rs2282158	0.82[CHB][hapmap]
rs33962342	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs3739654	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3818705	0.88[CHB][hapmap]
rs4556138	0.85[EUR][1000 genomes]
rs4740844	0.82[CHB][hapmap]
rs4742201	0.87[CHB][hapmap]
rs4742202	0.82[CHB][hapmap]
rs504698	0.88[EUR][1000 genomes]
rs530722	0.85[EUR][1000 genomes]
rs569866	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6477086	0.87[EUR][1000 genomes]
rs6477087	0.93[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66509816	0.85[ASN][1000 genomes]
rs73401025	0.88[ASN][1000 genomes]
rs7847675	0.89[ASN][1000 genomes]
rs7848831	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7852539	0.82[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7857628	0.82[CHB][hapmap]
rs7860966	0.82[EUR][1000 genomes]
rs7861073	0.82[EUR][1000 genomes]
rs7861559	0.82[EUR][1000 genomes]
rs7865955	0.82[CHB][hapmap]
rs7873756	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	esv3366333	chr9:6497322-6498037	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7029772	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6459400-6501800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:6463600-6518400	Weak transcription	Fetal Brain Male	brain
3	chr9:6471600-6501800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:6471600-6504600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:6472200-6508200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:6473000-6499600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:6473800-6498400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:6473800-6506200	Weak transcription	Small Intestine	intestine
9	chr9:6474800-6502800	Strong transcription	Dnd41	blood
10	chr9:6475200-6503000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr9:6475400-6508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:6475400-6508400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:6475400-6508800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr9:6475400-6508800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:6475800-6509000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:6475800-6510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:6476000-6509400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:6477600-6497800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:6477600-6507800	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:6477800-6511000	Weak transcription	Fetal Heart	heart
21	chr9:6478000-6498200	Weak transcription	Brain Angular Gyrus	brain
22	chr9:6478200-6498000	Weak transcription	Esophagus	oesophagus
23	chr9:6478400-6503400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:6478600-6498600	Weak transcription	Spleen	Spleen
25	chr9:6480200-6508400	Weak transcription	Stomach Mucosa	stomach
26	chr9:6481600-6502800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr9:6483200-6498000	Strong transcription	HMEC	breast
28	chr9:6484000-6498600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:6484400-6498200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:6484600-6497800	Weak transcription	Pancreas	Pancrea
31	chr9:6484600-6501800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:6485800-6498000	Weak transcription	Gastric	stomach
33	chr9:6487600-6498000	Weak transcription	Brain Anterior Caudate	brain
34	chr9:6487600-6499600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr9:6487600-6510600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr9:6488000-6497600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:6488200-6497800	Weak transcription	Brain Germinal Matrix	brain
38	chr9:6488200-6497800	Weak transcription	Lung	lung
39	chr9:6488200-6497800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:6488200-6498400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:6488800-6498200	Weak transcription	Fetal Brain Female	brain
42	chr9:6488800-6498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:6488800-6498600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:6489200-6501600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:6489200-6503000	Strong transcription	Primary B cells from cord blood	blood
46	chr9:6490400-6498200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:6490600-6498200	Weak transcription	Fetal Stomach	stomach
48	chr9:6491800-6498400	Weak transcription	Fetal Intestine Small	intestine
49	chr9:6492200-6497600	Weak transcription	Colon Smooth Muscle	Colon
50	chr9:6492800-6508800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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