Variant report

Variant	rs4351475
Chromosome Location	chr9:71990645-71990646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1034238	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11139245	0.81[JPT][hapmap]
rs11139246	0.81[JPT][hapmap]
rs12003507	0.87[ASN][1000 genomes]
rs12551899	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13284247	0.87[ASN][1000 genomes]
rs13284677	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13285975	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13290847	0.80[JPT][hapmap]
rs13290881	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13291679	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs13296504	0.81[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13297121	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13298045	0.85[ASN][1000 genomes]
rs13300133	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475641	0.80[JPT][hapmap]
rs17412941	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs1855529	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs2253778	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs34133536	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34295676	0.88[ASN][1000 genomes]
rs34672585	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4307408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4554547	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744884	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs4744885	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs4744893	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60284429	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028920	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7033124	0.88[ASN][1000 genomes]
rs7853058	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7855000	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7867609	0.95[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs867366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4351475	CSGALNACT2	trans	cerebellum	SCAN
rs4351475	GRIK2	trans	parietal	SCAN
rs4351475	C9orf71	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71962200-71994200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:71963200-71991800	Weak transcription	Pancreas	Pancrea
3	chr9:71972600-71991800	Weak transcription	Right Atrium	heart
4	chr9:71972800-71991400	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:71977400-71992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:71978800-71991600	Weak transcription	Left Ventricle	heart
7	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
9	chr9:71985400-71994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:71985600-71991000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:71985600-71991200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:71985600-71991400	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:71985600-71992400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:71986000-71990800	Weak transcription	HSMMtube	muscle
16	chr9:71986600-71991000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:71986600-71991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:71986600-71991000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:71986600-71991200	Weak transcription	Stomach Mucosa	stomach
20	chr9:71986600-71991600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:71986600-71991800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:71986600-71991800	Weak transcription	Gastric	stomach
23	chr9:71986600-71992200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:71986600-72002600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:71986800-71991000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:71986800-71991000	Weak transcription	Osteobl	bone
27	chr9:71986800-71991200	Weak transcription	NH-A	brain
28	chr9:71986800-71994200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:71987000-71991000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:71987000-71991000	Weak transcription	HUVEC	blood vessel
31	chr9:71987000-71991400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:71987000-71992200	Weak transcription	Brain Angular Gyrus	brain
33	chr9:71987600-71991800	Weak transcription	Psoas Muscle	Psoas
34	chr9:71988800-71998600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr9:71989000-72002800	Weak transcription	Brain Substantia Nigra	brain
36	chr9:71989200-71992200	Enhancers	Ovary	ovary
37	chr9:71989600-71991600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr9:71989600-71991800	Weak transcription	Right Ventricle	heart
39	chr9:71989600-71997000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr9:71989800-71990800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:71989800-71991200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr9:71989800-71994000	Genic enhancers	Fetal Heart	heart
43	chr9:71990000-71991800	Weak transcription	Fetal Stomach	stomach
44	chr9:71990000-71992200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:71990000-71992200	Enhancers	HMEC	breast
46	chr9:71990200-71991400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:71990200-71991600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr9:71990200-71992400	Enhancers	NHEK	skin
49	chr9:71990600-71992400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:71990600-71992600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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