Variant report

Variant	rs2997657
Chromosome Location	chr9:72662689-72662690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11141566	0.92[ASN][1000 genomes]
rs11141672	0.88[ASN][1000 genomes]
rs11141697	0.86[ASN][1000 genomes]
rs11142141	0.82[CHB][hapmap]
rs12349576	0.84[ASN][1000 genomes]
rs12352964	0.90[ASN][1000 genomes]
rs1927104	0.83[ASN][1000 genomes]
rs28462281	0.92[ASN][1000 genomes]
rs2997665	0.88[ASN][1000 genomes]
rs3015234	0.82[ASN][1000 genomes]
rs3015237	0.88[ASN][1000 genomes]
rs3015239	0.91[ASN][1000 genomes]
rs4237238	0.91[ASN][1000 genomes]
rs4237239	0.91[ASN][1000 genomes]
rs4237240	0.91[ASN][1000 genomes]
rs4367620	0.88[ASN][1000 genomes]
rs4744586	0.88[ASN][1000 genomes]
rs4744970	0.88[ASN][1000 genomes]
rs4744971	0.91[ASN][1000 genomes]
rs4744972	0.88[ASN][1000 genomes]
rs4744979	0.86[ASN][1000 genomes]
rs4744981	0.84[ASN][1000 genomes]
rs6559970	0.88[ASN][1000 genomes]
rs7035878	0.87[ASN][1000 genomes]
rs7045153	0.91[ASN][1000 genomes]
rs755778	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7853094	0.84[ASN][1000 genomes]
rs7873075	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2997657	MAMDC2	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72659600-72663400	Weak transcription	Spleen	Spleen
2	chr9:72659600-72663800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:72659800-72663800	Weak transcription	Fetal Heart	heart
4	chr9:72659800-72664200	Weak transcription	Brain Germinal Matrix	brain
5	chr9:72660000-72663600	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:72660000-72663800	Weak transcription	Brain Anterior Caudate	brain
7	chr9:72660000-72663800	Weak transcription	Osteobl	bone
8	chr9:72660000-72664600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:72660000-72665200	Transcr. at gene 5' and 3'	HSMMtube	muscle
10	chr9:72660000-72668400	Weak transcription	HUVEC	blood vessel
11	chr9:72660200-72663600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:72660200-72663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:72660200-72663600	Weak transcription	Psoas Muscle	Psoas
14	chr9:72660200-72663600	Weak transcription	NHLF	lung
15	chr9:72660200-72664000	Weak transcription	Right Ventricle	heart
16	chr9:72660200-72668200	Weak transcription	Pancreas	Pancrea
17	chr9:72660200-72668400	Weak transcription	Gastric	stomach
18	chr9:72660400-72663000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
19	chr9:72660400-72663600	Weak transcription	NHDF-Ad	bronchial
20	chr9:72660600-72664000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr9:72661000-72665000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:72661400-72662800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:72661400-72663200	Weak transcription	Left Ventricle	heart
24	chr9:72661400-72663800	Weak transcription	Fetal Lung	lung
25	chr9:72661400-72664000	Weak transcription	Fetal Brain Female	brain
26	chr9:72661600-72663200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:72661600-72663200	Weak transcription	Lung	lung
28	chr9:72661600-72663600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:72661600-72663600	Weak transcription	Esophagus	oesophagus
30	chr9:72661600-72663800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:72661600-72663800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr9:72661600-72663800	Weak transcription	Fetal Stomach	stomach
33	chr9:72661600-72664000	Weak transcription	Fetal Intestine Small	intestine
34	chr9:72661600-72671600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:72661600-72672000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:72661800-72662800	Weak transcription	Right Atrium	heart
37	chr9:72661800-72662800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:72661800-72662800	Weak transcription	HSMM	muscle
39	chr9:72661800-72663600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:72661800-72663600	Weak transcription	Placenta	Placenta
41	chr9:72661800-72663800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:72661800-72663800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr9:72661800-72663800	Weak transcription	NH-A	brain
44	chr9:72661800-72664000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:72661800-72664000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:72661800-72664000	Weak transcription	Aorta	Aorta
47	chr9:72661800-72664400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr9:72661800-72665000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:72661800-72665400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:72661800-72665800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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