Variant report

Variant	rs1013397
Chromosome Location	chr4:143375877-143375878
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	chr4:143374144..143376062-chr4:143381954..143384712,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10012476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015184	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015271	0.90[EUR][1000 genomes]
rs12642500	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12643136	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12644565	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12646243	0.87[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12649139	0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1364917	0.87[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes]
rs1364918	0.87[CEU][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes]
rs1364919	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1364920	0.81[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes]
rs1364926	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1425534	0.87[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1425535	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1425538	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1603584	0.85[ASN][1000 genomes]
rs17016170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17016195	0.89[EUR][1000 genomes]
rs17016207	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17016248	1.00[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17016284	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17016304	1.00[ASW][hapmap];0.87[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2042644	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2113997	0.82[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2162108	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2322705	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2322706	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2322796	0.84[AMR][1000 genomes]
rs28510314	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28823374	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28850298	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28861843	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34900920	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3913164	1.00[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs3913165	0.89[EUR][1000 genomes]
rs4345256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57724540	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59784151	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs60004938	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6822263	0.85[CEU][hapmap]
rs6823362	0.83[AMR][1000 genomes]
rs7662794	0.89[EUR][1000 genomes]
rs7668133	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7672965	0.87[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7695918	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7699408	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9308152	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931637	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs979511	1.00[CEU][hapmap];0.83[CHD][hapmap]
rs9986090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998089	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1013397	HHIP	cis	parietal	SCAN
rs1013397	INPP4B	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143367000-143392600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:143369200-143410600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:143369400-143376400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:143371400-143376400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:143371600-143400800	Weak transcription	Aorta	Aorta
6	chr4:143374200-143379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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