Variant report

Variant	rs10907376
Chromosome Location	chr1:223567803-223567804
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	chr1:223534957..223537393-chr1:223566287..223567830,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143502	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10495206	0.83[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs10495207	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11261264	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11261270	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12123148	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12134824	0.81[AMR][1000 genomes]
rs12140453	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12564615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1400959	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap]
rs1547788	0.84[EUR][1000 genomes]
rs1619227	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs1713220	0.81[EUR][1000 genomes]
rs17162008	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17162072	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17163827	0.83[EUR][1000 genomes]
rs17163828	0.80[EUR][1000 genomes]
rs17163831	0.80[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs17479856	0.83[JPT][hapmap]
rs17480087	0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs17480344	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs17518349	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs17518363	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap]
rs17538964	0.83[JPT][hapmap]
rs17539269	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs17539583	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17578168	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17578203	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1772280	0.96[EUR][1000 genomes]
rs2138966	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2459849	0.81[EUR][1000 genomes]
rs2487521	0.81[EUR][1000 genomes]
rs2678377	0.81[EUR][1000 genomes]
rs34150324	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59355120	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838210	0.82[EUR][1000 genomes]
rs61838229	0.82[EUR][1000 genomes]
rs61838230	0.82[EUR][1000 genomes]
rs61838231	0.82[EUR][1000 genomes]
rs61838238	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61838239	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61838240	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61838243	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61838250	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61838252	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61839867	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61839875	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61839876	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839877	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839878	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839879	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604709	0.88[EUR][1000 genomes]
rs7555607	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs870486	0.82[EUR][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	nsv832670	chr1:223561771-223683381	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv4687	chr1:223565080-223610362	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv517708	chr1:223567267-223567803	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10907376	SUSD4	cis	Heart Left Ventricle	GTEx
rs10907376	SUSD4	cis	parietal	SCAN
rs10907376	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223566800-223568600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:223567200-223568000	ZNF genes & repeats	Lung	lung
3	chr1:223567400-223568000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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