Variant report

Variant	rs597420
Chromosome Location	chr2:97070353-97070354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1081711	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1081713	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2579505	0.80[CEU][hapmap]
rs582014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs583705	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs585781	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs596069	0.92[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs605175	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs607302	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs611943	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs618454	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs631033	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631746	0.87[EUR][1000 genomes]
rs654224	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs655101	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs670498	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs674920	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs675239	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676007	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs679414	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs687950	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772156	0.88[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs772159	0.84[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs772160	0.81[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs772161	0.84[EUR][1000 genomes]
rs772167	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs772173	0.88[CEU][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs772174	0.84[CEU][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs772177	0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv3416952	chr2:97043127-97076830	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3404635	chr2:97068275-97070773	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs597420	ITPRIPL1	cis	Esophagus Mucosa	GTEx
rs597420	ADRA2B	cis	cerebellum	SCAN
rs597420	LOC285033	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97063000-97073200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:97065600-97073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:97065800-97073200	Weak transcription	Gastric	stomach
4	chr2:97065800-97073400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:97066000-97070800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:97066200-97073000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:97066600-97070400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:97069200-97071800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr2:97069200-97072000	Enhancers	Fetal Muscle Leg	muscle
10	chr2:97069400-97070600	Enhancers	Esophagus	oesophagus
11	chr2:97069400-97074800	Enhancers	Fetal Thymus	thymus
12	chr2:97069400-97075000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:97069600-97070400	Weak transcription	Pancreas	Pancrea
14	chr2:97069600-97070600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:97069600-97070800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:97069600-97071400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:97070200-97070600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:97070200-97071000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:97070200-97071200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr2:97070200-97073000	Enhancers	Thymus	Thymus

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