Variant report

Variant	rs2339289
Chromosome Location	chr8:91937320-91937321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:91935926..91938276-chr8:92081744..92084035,2	MCF-7	breast:
2	chr8:91781884..91783828-chr8:91937169..91939199,2	MCF-7	breast:
3	chr8:91932705..91934406-chr8:91937301..91938900,2	MCF-7	breast:
4	chr8:91933857..91937511-chr8:91939671..91942418,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253738	Chromatin interaction
ENSG00000155100	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1002583	0.82[AMR][1000 genomes]
rs1003996	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10086609	0.90[GIH][hapmap];0.84[TSI][hapmap]
rs10108486	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10108616	0.82[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs10112439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1011254	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1055146	0.84[MEX][hapmap]
rs10956781	0.90[GIH][hapmap];0.84[TSI][hapmap]
rs10956782	0.90[GIH][hapmap];0.84[TSI][hapmap]
rs1125229	0.88[MEX][hapmap];0.84[TSI][hapmap]
rs1160329	0.88[MEX][hapmap]
rs12675931	0.92[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13265644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13276591	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs1352159	0.84[MEX][hapmap]
rs1354519	0.82[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1354520	0.82[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs1386107	0.82[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs1386111	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1386112	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1463920	0.90[GIH][hapmap];0.84[TSI][hapmap]
rs1486465	0.94[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1504795	0.82[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1542666	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1552397	0.88[MEX][hapmap]
rs16905444	0.90[GIH][hapmap];0.84[TSI][hapmap]
rs16905571	0.82[CEU][hapmap]
rs2054805	0.89[CEU][hapmap];0.94[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2054806	0.84[MEX][hapmap]
rs2101378	0.88[MEX][hapmap]
rs2129260	0.88[MEX][hapmap];0.84[TSI][hapmap]
rs2129261	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255173	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2339291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631012	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2631014	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2631017	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631024	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631030	0.89[ASN][1000 genomes]
rs2631033	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2677573	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2677580	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2740776	0.87[EUR][1000 genomes]
rs2740782	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2740788	0.84[MEX][hapmap]
rs2740791	0.87[MEX][hapmap]
rs2740795	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2740799	0.94[CEU][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4448231	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4634599	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6471261	0.88[MEX][hapmap];0.84[TSI][hapmap]
rs6994971	0.90[GIH][hapmap];0.84[TSI][hapmap]
rs7005565	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7018395	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7818155	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7825360	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7828122	0.89[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs7829663	0.83[MEX][hapmap]
rs7831333	0.84[MEX][hapmap]
rs997898	0.84[MEX][hapmap]
rs997899	0.88[MEX][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	nsv1028628	chr8:91680968-92418954	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv539672	chr8:91680968-92418954	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv891185	chr8:91923776-92056288	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2339289	INTS8	cis	cerebellum	SCAN
rs2339289	TP53INP1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:91916400-91953000	Weak transcription	Aorta	Aorta
2	chr8:91926400-91948800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr8:91926600-91948400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr8:91926800-91948400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr8:91929400-91948200	Weak transcription	Brain Anterior Caudate	brain
6	chr8:91929800-91948000	Weak transcription	Brain Angular Gyrus	brain
7	chr8:91932600-91937600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr8:91932600-91938800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr8:91932800-91937600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr8:91933600-91943200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr8:91934400-91939800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr8:91934800-91952200	Weak transcription	Colon Smooth Muscle	Colon
13	chr8:91935200-91948400	Weak transcription	Fetal Brain Male	brain
14	chr8:91935800-91947600	Weak transcription	Brain Hippocampus Middle	brain
15	chr8:91936400-91939800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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