Variant report

Variant	rs1983352
Chromosome Location	chr2:99454227-99454228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99344923..99349258-chr2:99450100..99455296,6	MCF-7	breast:
2	chr2:99265598..99266647-chr2:99453141..99454628,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10169003	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10172158	0.87[EUR][1000 genomes]
rs10181972	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10188156	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123755	0.87[EUR][1000 genomes]
rs11887536	0.87[EUR][1000 genomes]
rs11893888	0.82[EUR][1000 genomes]
rs12468024	0.87[EUR][1000 genomes]
rs12712033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12712034	0.90[CHB][hapmap];0.81[YRI][hapmap]
rs12712035	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712036	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12712038	0.87[EUR][1000 genomes]
rs12712039	0.85[EUR][1000 genomes]
rs12992214	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13004923	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13389386	0.90[JPT][hapmap]
rs1356424	0.84[CEU][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1568213	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs1581250	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1581251	0.87[EUR][1000 genomes]
rs1878585	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2276604	0.84[JPT][hapmap]
rs2280256	0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4263159	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4850888	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851162	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851163	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851167	0.87[EUR][1000 genomes]
rs4851170	0.87[EUR][1000 genomes]
rs4851171	0.87[EUR][1000 genomes]
rs6542838	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542839	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs6711022	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6713991	0.96[CEU][hapmap];0.90[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6714243	0.87[EUR][1000 genomes]
rs6717372	0.85[EUR][1000 genomes]
rs6719634	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6724477	0.81[GIH][hapmap]
rs6726156	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6733011	0.97[ASN][1000 genomes]
rs6757099	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7579189	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608889	0.84[JPT][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs925887	0.84[GIH][hapmap];0.80[TSI][hapmap]
rs981601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981602	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1983352	LIPT1	cis	parietal	SCAN
rs1983352	TEKT4	cis	parietal	SCAN
rs1983352	FAHD2B	cis	parietal	SCAN
rs1983352	MITD1	cis	parietal	SCAN
rs1983352	TSGA10	cis	cerebellum	SCAN
rs1983352	C2orf15	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99440000-99460600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:99440400-99463400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:99450000-99454600	Weak transcription	Brain Angular Gyrus	brain
4	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
5	chr2:99450600-99455200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:99450600-99455200	Weak transcription	HMEC	breast
7	chr2:99450600-99456200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:99450800-99462800	Weak transcription	Gastric	stomach
9	chr2:99451000-99456400	Weak transcription	Lung	lung
10	chr2:99453200-99457000	Weak transcription	Esophagus	oesophagus
11	chr2:99453200-99460600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:99453200-99473200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:99454000-99455200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:99454000-99455200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:99454000-99456400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:99454000-99456400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:99454200-99459000	Weak transcription	A549	lung

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